Mapping Step 2 about wasp HOT 14 CLOSED

What is written to stdout and stderr? There might not be an error, but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly [email protected] wrote:

The output files are empty but I receive no error message or anything. I
have no idea why my accepted_hits.quality.remap.num.gz and remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

from wasp.

Thank you so much for getting back to me, I greatly appreciate your help! I can not seem to find stderr anywhere. I’ve looked everywhere. Am I supposed to pull it out with a command in terminal because the file doesn’t seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new to this :/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn [email protected] wrote:

What is written to stdout and stderr? There might not be an error, but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly [email protected] wrote:

The output files are empty but I receive no error message or anything. I
have no idea why my accepted_hits.quality.remap.num.gz and remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub #8 (comment).

from wasp.

Ah sorry for the confusion. Earlier you sent me what was printed when you
ran the second step, but there was an error. I would like what was printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly [email protected] wrote:

Thank you so much for getting back to me, I greatly appreciate your help!
I can not seem to find stderr anywhere. I’ve looked everywhere. Am I
supposed to pull it out with a command in terminal because the file doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new to this :/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an error, but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly [email protected]
wrote:

The output files are empty but I receive no error message or anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

from wasp.

I didn’t save it but I didn’t receive an error messages after running step 2 on Mapping and even said Finished! when it was done.

My command $ python /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files
Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn [email protected] wrote:

Ah sorry for the confusion. Earlier you sent me what was printed when you
ran the second step, but there was an error. I would like what was printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly [email protected] wrote:

Thank you so much for getting back to me, I greatly appreciate your help!
I can not seem to find stderr anywhere. I’ve looked everywhere. Am I
supposed to pull it out with a command in terminal because the file doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new to this :/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an error, but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly [email protected]
wrote:

The output files are empty but I receive no error message or anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

—
Reply to this email directly or view it on GitHub #8 (comment).

from wasp.

That is strange. Have you checked to make sure that the SNP files you sent
it aren't empty? There should also be a *.keep.bam file which contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly [email protected] wrote:

I didn’t save it but I didn’t receive an error messages after running step
2 on Mapping and even said Finished! when it was done.

My command $ python
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files
Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn [email protected]
wrote:

Ah sorry for the confusion. Earlier you sent me what was printed when you
ran the second step, but there was an error. I would like what was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly [email protected]
wrote:

Thank you so much for getting back to me, I greatly appreciate your
help!
I can not seem to find stderr anywhere. I’ve looked everywhere. Am I
supposed to pull it out with a command in terminal because the file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new to this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly [email protected]
wrote:

The output files are empty but I receive no error message or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90224346>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

from wasp.

My SNP files are filled and are done correctly with position, ref allele, alt allele each file is ~ 3-20MB and the accepted_hits.keep.bam is 7.7MB

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn [email protected] wrote:

That is strange. Have you checked to make sure that the SNP files you sent
it aren't empty? There should also be a *.keep.bam file which contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly [email protected] wrote:

I didn’t save it but I didn’t receive an error messages after running step
2 on Mapping and even said Finished! when it was done.

My command $ python
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files
Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn [email protected]
wrote:

Ah sorry for the confusion. Earlier you sent me what was printed when you
ran the second step, but there was an error. I would like what was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly [email protected]
wrote:

Thank you so much for getting back to me, I greatly appreciate your
help!
I can not seem to find stderr anywhere. I’ve looked everywhere. Am I
supposed to pull it out with a command in terminal because the file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new to this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly [email protected]
wrote:

The output files are empty but I receive no error message or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90224346>.

—
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#8 (comment).

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from wasp.

Do the chr#.snps.txt.gz files need to contain a header? "position RefAllele AltAllele" because my chr# files do not contain a header.

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn [email protected] wrote:

That is strange. Have you checked to make sure that the SNP files you sent
it aren't empty? There should also be a *.keep.bam file which contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly [email protected] wrote:

I didn’t save it but I didn’t receive an error messages after running step
2 on Mapping and even said Finished! when it was done.

My command $ python
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files
Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn [email protected]
wrote:

Ah sorry for the confusion. Earlier you sent me what was printed when you
ran the second step, but there was an error. I would like what was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly [email protected]
wrote:

Thank you so much for getting back to me, I greatly appreciate your
help!
I can not seem to find stderr anywhere. I’ve looked everywhere. Am I
supposed to pull it out with a command in terminal because the file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new to this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly [email protected]
wrote:

The output files are empty but I receive no error message or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90224346>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

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from wasp.

They shouldn't contain headers. How large was your originally mapped bam?

On Mon, Apr 6, 2015 at 3:37 PM, Kimberly [email protected] wrote:

Do the chr#.snps.txt.gz files need to contain a header? "position
RefAllele AltAllele" because my chr# files do not contain a header.

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn [email protected]
wrote:

That is strange. Have you checked to make sure that the SNP files you
sent
it aren't empty? There should also be a *.keep.bam file which contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly [email protected]
wrote:

I didn’t save it but I didn’t receive an error messages after running
step
2 on Mapping and even said Finished! when it was done.

My command $ python

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files
Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn <
[email protected]>
wrote:

Ah sorry for the confusion. Earlier you sent me what was printed
when you
ran the second step, but there was an error. I would like what was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly [email protected]
wrote:

Thank you so much for getting back to me, I greatly appreciate your
help!
I can not seem to find stderr anywhere. I’ve looked everywhere. Am
I
supposed to pull it out with a command in terminal because the file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new to
this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an
error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly <
[email protected]>
wrote:

The output files are empty but I receive no error message or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

—
Reply to this email directly or view it on GitHub
<#8 (comment)
.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90224346>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

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Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90230563>.

—
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#8 (comment).

from wasp.

My original mapped bam from running TopHat is 25.7MB

On Apr 6, 2015, at 1:53 PM, Bryce van de Geijn [email protected] wrote:

They shouldn't contain headers. How large was your originally mapped bam?

On Mon, Apr 6, 2015 at 3:37 PM, Kimberly [email protected] wrote:

Do the chr#.snps.txt.gz files need to contain a header? "position
RefAllele AltAllele" because my chr# files do not contain a header.

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn [email protected]
wrote:

That is strange. Have you checked to make sure that the SNP files you
sent
it aren't empty? There should also be a *.keep.bam file which contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly [email protected]
wrote:

I didn’t save it but I didn’t receive an error messages after running
step
2 on Mapping and even said Finished! when it was done.

My command $ python

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files
Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn <
[email protected]>
wrote:

Ah sorry for the confusion. Earlier you sent me what was printed
when you
ran the second step, but there was an error. I would like what was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly [email protected]
wrote:

Thank you so much for getting back to me, I greatly appreciate your
help!
I can not seem to find stderr anywhere. I’ve looked everywhere. Am
I
supposed to pull it out with a command in terminal because the file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new to
this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an
error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly <
[email protected]>
wrote:

The output files are empty but I receive no error message or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

—
Reply to this email directly or view it on GitHub
<#8 (comment)
.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90224346>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90230563>.

—
Reply to this email directly or view it on GitHub
#8 (comment).

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Reply to this email directly or view it on GitHub #8 (comment).

from wasp.

That is unsorted? The sorted bam files often end up smaller. Are you SNPs
sorted?

On Mon, Apr 6, 2015 at 3:57 PM, Kimberly [email protected] wrote:

My original mapped bam from running TopHat is 25.7MB

On Apr 6, 2015, at 1:53 PM, Bryce van de Geijn [email protected]
wrote:

They shouldn't contain headers. How large was your originally mapped bam?

On Mon, Apr 6, 2015 at 3:37 PM, Kimberly [email protected]
wrote:

Do the chr#.snps.txt.gz files need to contain a header? "position
RefAllele AltAllele" because my chr# files do not contain a header.

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn <
[email protected]>
wrote:

That is strange. Have you checked to make sure that the SNP files you
sent
it aren't empty? There should also be a *.keep.bam file which
contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly [email protected]
wrote:

I didn’t save it but I didn’t receive an error messages after
running
step
2 on Mapping and even said Finished! when it was done.

My command $ python

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files

Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn <
[email protected]>
wrote:

Ah sorry for the confusion. Earlier you sent me what was printed
when you
ran the second step, but there was an error. I would like what
was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly <
[email protected]>
wrote:

Thank you so much for getting back to me, I greatly appreciate
your
help!
I can not seem to find stderr anywhere. I’ve looked
everywhere. Am
I
supposed to pull it out with a command in terminal because the
file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new
to
this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an
error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly <
[email protected]>
wrote:

The output files are empty but I receive no error message
or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <

https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

—
Reply to this email directly or view it on GitHub
<
#8 (comment)
.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90224346>.

—
Reply to this email directly or view it on GitHub
<#8 (comment)
.

—
Reply to this email directly or view it on GitHub <
https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90230563>.

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#8 (comment).

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#8 (comment).

from wasp.

I’m sorry I don’t fully understand
accepted_hits.sort.bam 25.7MB
accepted_hits.bam 25.7MB

and I don’t know if my SNPs are sorted or not.

I’m confused.

Here is my TopHat command $ ./tophat --no-coverage-search -o /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out -p 6 -G /Users/olneykimberly/Desktop/1_code/gencode.v18.annotation.gtf /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/GenomicReference/build37_used_by_cg /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SRR_files/SRR035022.filt.fastq

Output files from TopHat:

On Apr 6, 2015, at 2:02 PM, Bryce van de Geijn [email protected] wrote:

That is unsorted? The sorted bam files often end up smaller. Are you SNPs
sorted?

On Mon, Apr 6, 2015 at 3:57 PM, Kimberly [email protected] wrote:

My original mapped bam from running TopHat is 25.7MB

On Apr 6, 2015, at 1:53 PM, Bryce van de Geijn [email protected]
wrote:

They shouldn't contain headers. How large was your originally mapped bam?

On Mon, Apr 6, 2015 at 3:37 PM, Kimberly [email protected]
wrote:

Do the chr#.snps.txt.gz files need to contain a header? "position
RefAllele AltAllele" because my chr# files do not contain a header.

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn <
[email protected]>
wrote:

That is strange. Have you checked to make sure that the SNP files you
sent
it aren't empty? There should also be a *.keep.bam file which
contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly [email protected]
wrote:

I didn’t save it but I didn’t receive an error messages after
running
step
2 on Mapping and even said Finished! when it was done.

My command $ python

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files

Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn <
[email protected]>
wrote:

Ah sorry for the confusion. Earlier you sent me what was printed
when you
ran the second step, but there was an error. I would like what
was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly <
[email protected]>
wrote:

Thank you so much for getting back to me, I greatly appreciate
your
help!
I can not seem to find stderr anywhere. I’ve looked
everywhere. Am
I
supposed to pull it out with a command in terminal because the
file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m new
to
this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be an
error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly <
[email protected]>
wrote:

The output files are empty but I receive no error message
or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

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from wasp.

I'm trying to get a sense of how many reads are kept after step 2. It
looks like it's only ~1/4. If the SNPs aren't sorted then the script
breaks down, but I believe there should be a warning message. Since the
files are pretty small, do you mind sending me accepted_hits.bam file and
the SNP files you are using? It might be faster if I take a look at them.

On Mon, Apr 6, 2015 at 4:10 PM, Kimberly [email protected] wrote:

I’m sorry I don’t fully understand
accepted_hits.sort.bam 25.7MB
accepted_hits.bam 25.7MB

and I don’t know if my SNPs are sorted or not.

I’m confused.

Here is my TopHat command $ ./tophat --no-coverage-search -o
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out
-p 6 -G /Users/olneykimberly/Desktop/1_code/gencode.v18.annotation.gtf
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/GenomicReference/build37_used_by_cg
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SRR_files/SRR035022.filt.fastq

Output files from TopHat:

On Apr 6, 2015, at 2:02 PM, Bryce van de Geijn [email protected]
wrote:

That is unsorted? The sorted bam files often end up smaller. Are you SNPs
sorted?

On Mon, Apr 6, 2015 at 3:57 PM, Kimberly [email protected]
wrote:

My original mapped bam from running TopHat is 25.7MB

On Apr 6, 2015, at 1:53 PM, Bryce van de Geijn <
[email protected]>
wrote:

They shouldn't contain headers. How large was your originally mapped
bam?

On Mon, Apr 6, 2015 at 3:37 PM, Kimberly [email protected]
wrote:

Do the chr#.snps.txt.gz files need to contain a header? "position
RefAllele AltAllele" because my chr# files do not contain a header.

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn <
[email protected]>
wrote:

That is strange. Have you checked to make sure that the SNP
files you
sent
it aren't empty? There should also be a *.keep.bam file which
contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly <
[email protected]>
wrote:

I didn’t save it but I didn’t receive an error messages after
running
step
2 on Mapping and even said Finished! when it was done.

My command $ python

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files

Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn <
[email protected]>
wrote:

Ah sorry for the confusion. Earlier you sent me what was
printed
when you
ran the second step, but there was an error. I would like
what
was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly <
[email protected]>
wrote:

Thank you so much for getting back to me, I greatly
appreciate
your
help!
I can not seem to find stderr anywhere. I’ve looked
everywhere. Am
I
supposed to pull it out with a command in terminal because
the
file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m
new
to
this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be
an
error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly <
[email protected]>
wrote:

The output files are empty but I receive no error
message
or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz
and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
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https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

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<
#8 (comment)
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#8 (comment).

from wasp.

Attachments available until May 6, 2015
Absolutely! Thank you again for helping me :)

Here is my accepted_hits.bam. The SNP files are too large to send over all of them so I selected chr13 to send since it’s one of the smaller chromosomes. If you need all of them I’d be happy to send them over I’ll just have to send multiple emails if that’s okay.

Click to Download
https://www.icloud.com/attachment/?u=https%3A%2F%2Fs3-us-ore-108-prod.digitalhub.com%2FB%2FAbqlPCv26oQCcKCINwVC3qauaKYdAUGN7IL0W-8D4scxYlKWzm_cQXym%2F%24%7Bf%7D%3Fo%3DApvqOcNn3B5gPjvI-fiaRDiUkc8hS0mt8sORBJ__gNaS%26v%3D1%26x%3D3%26a%3DBQS6Kf_Kboj_A57jKgEA_wHIAP8eR8AA%26e%3D1430950890%26k%3D%24%7Buk%7D%26r%3D0A1C395C-E349-48E7-B99F-1906B89E2631-1%26ckc%3Dcom.apple.largeattachment%26ckz%3DBAA989C0-BC7C-4E78-B147-B1DA248F6742%26z%3Dhttps%253A%252F%252Fp21-content.icloud.com%253A443%26s%3DxpTeI5b8SVtb64O0iTbR0msRgj8&uk=GytMDZ9eT1F_d7VKCuZTcQ&f=accepted_hits.bam&sz=25691867accepted_hits.bam
25.7 MB

Click to Download
https://www.icloud.com/attachment/?u=https%3A%2F%2Fs3-us-ore-108-prod.digitalhub.com%2FB%2FAR7EzD_NUVVYWpNuutUqWajbcsJKAVQz2G8SPUXPbw-gF7yPHQN-KfZ0%2F%24%7Bf%7D%3Fo%3DAgpe1BfbfECEghNWP2mRGe8T67N-HKRs21HKBmLAC7Yk%26v%3D1%26x%3D3%26a%3DBbTHZwJoDZ8EA57jKgEA_wHIAP8q07vU%26e%3D1430950891%26k%3D%24%7Buk%7D%26r%3DAB33538D-541D-4A10-ABF9-051AD92EB2FC-1%26ckc%3Dcom.apple.largeattachment%26ckz%3DBAA989C0-BC7C-4E78-B147-B1DA248F6742%26z%3Dhttps%253A%252F%252Fp21-content.icloud.com%253A443%26s%3Dx8jRpbd0xoRxUACD1vN6pzsrxmo&uk=pEqaG4NBH8Cpt1SniqBoQw&f=chr13.snps.txt.gz&sz=7050476chr13.snps.txt.gz
7.1 MB

On Apr 6, 2015, at 2:27 PM, Bryce van de Geijn <[email protected] mailto:[email protected]> wrote:

I'm trying to get a sense of how many reads are kept after step 2. It
looks like it's only ~1/4. If the SNPs aren't sorted then the script
breaks down, but I believe there should be a warning message. Since the
files are pretty small, do you mind sending me accepted_hits.bam file and
the SNP files you are using? It might be faster if I take a look at them.

On Mon, Apr 6, 2015 at 4:10 PM, Kimberly <[email protected] mailto:[email protected]> wrote:

I’m sorry I don’t fully understand
accepted_hits.sort.bam 25.7MB
accepted_hits.bam 25.7MB

and I don’t know if my SNPs are sorted or not.

I’m confused.

Here is my TopHat command $ ./tophat --no-coverage-search -o
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out
-p 6 -G /Users/olneykimberly/Desktop/1_code/gencode.v18.annotation.gtf
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/GenomicReference/build37_used_by_cg
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SRR_files/SRR035022.filt.fastq

Output files from TopHat:

On Apr 6, 2015, at 2:02 PM, Bryce van de Geijn <[email protected] mailto:[email protected]>
wrote:

That is unsorted? The sorted bam files often end up smaller. Are you SNPs
sorted?

On Mon, Apr 6, 2015 at 3:57 PM, Kimberly <[email protected] mailto:[email protected]>
wrote:

My original mapped bam from running TopHat is 25.7MB

On Apr 6, 2015, at 1:53 PM, Bryce van de Geijn <
[email protected] mailto:[email protected]>
wrote:

They shouldn't contain headers. How large was your originally mapped
bam?

On Mon, Apr 6, 2015 at 3:37 PM, Kimberly <[email protected] mailto:[email protected]>
wrote:

Do the chr#.snps.txt.gz files need to contain a header? "position
RefAllele AltAllele" because my chr# files do not contain a header.

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn <
[email protected] mailto:[email protected]>
wrote:

That is strange. Have you checked to make sure that the SNP
files you
sent
it aren't empty? There should also be a *.keep.bam file which
contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly <
[email protected] mailto:[email protected]>
wrote:

I didn’t save it but I didn’t receive an error messages after
running
step
2 on Mapping and even said Finished! when it was done.

My command $ python

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files

Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn <
[email protected] mailto:[email protected]>
wrote:

Ah sorry for the confusion. Earlier you sent me what was
printed
when you
ran the second step, but there was an error. I would like
what
was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly <
[email protected] mailto:[email protected]>
wrote:

Thank you so much for getting back to me, I greatly
appreciate
your
help!
I can not seem to find stderr anywhere. I’ve looked
everywhere. Am
I
supposed to pull it out with a command in terminal because
the
file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m
new
to
this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected] mailto:[email protected]> wrote:

What is written to stdout and stderr? There might not be
an
error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly <
[email protected] mailto:[email protected]>
wrote:

The output files are empty but I receive no error
message
or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz
and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
<#8 #8>.

—
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#8 (comment) https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

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#8 (comment) #8 (comment)
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from wasp.

Did you get my data I sent over?

On Apr 6, 2015, at 2:27 PM, Bryce van de Geijn [email protected] wrote:

I'm trying to get a sense of how many reads are kept after step 2. It
looks like it's only ~1/4. If the SNPs aren't sorted then the script
breaks down, but I believe there should be a warning message. Since the
files are pretty small, do you mind sending me accepted_hits.bam file and
the SNP files you are using? It might be faster if I take a look at them.

On Mon, Apr 6, 2015 at 4:10 PM, Kimberly [email protected] wrote:

I’m sorry I don’t fully understand
accepted_hits.sort.bam 25.7MB
accepted_hits.bam 25.7MB

and I don’t know if my SNPs are sorted or not.

I’m confused.

Here is my TopHat command $ ./tophat --no-coverage-search -o
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out
-p 6 -G /Users/olneykimberly/Desktop/1_code/gencode.v18.annotation.gtf
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/GenomicReference/build37_used_by_cg
/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SRR_files/SRR035022.filt.fastq

Output files from TopHat:

On Apr 6, 2015, at 2:02 PM, Bryce van de Geijn [email protected]
wrote:

That is unsorted? The sorted bam files often end up smaller. Are you SNPs
sorted?

On Mon, Apr 6, 2015 at 3:57 PM, Kimberly [email protected]
wrote:

My original mapped bam from running TopHat is 25.7MB

On Apr 6, 2015, at 1:53 PM, Bryce van de Geijn <
[email protected]>
wrote:

They shouldn't contain headers. How large was your originally mapped
bam?

On Mon, Apr 6, 2015 at 3:37 PM, Kimberly [email protected]
wrote:

Do the chr#.snps.txt.gz files need to contain a header? "position
RefAllele AltAllele" because my chr# files do not contain a header.

On Apr 6, 2015, at 1:29 PM, Bryce van de Geijn <
[email protected]>
wrote:

That is strange. Have you checked to make sure that the SNP
files you
sent
it aren't empty? There should also be a *.keep.bam file which
contains
reads that don't overlap SNPs. Is it empty as well?

On Mon, Apr 6, 2015 at 3:08 PM, Kimberly <
[email protected]>
wrote:

I didn’t save it but I didn’t receive an error messages after
running
step
2 on Mapping and even said Finished! when it was done.

My command $ python

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam

/Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files

Starting on chr1
starting on chr10
It did this for each chr#
chrX
chrY
Finished!

However my new files to remap are empty

On Apr 6, 2015, at 1:00 PM, Bryce van de Geijn <
[email protected]>
wrote:

Ah sorry for the confusion. Earlier you sent me what was
printed
when you
ran the second step, but there was an error. I would like
what
was
printed
when there wasn't an error. For example, "Starting chr1"....

On Mon, Apr 6, 2015 at 2:45 PM, Kimberly <
[email protected]>
wrote:

Thank you so much for getting back to me, I greatly
appreciate
your
help!
I can not seem to find stderr anywhere. I’ve looked
everywhere. Am
I
supposed to pull it out with a command in terminal because
the
file
doesn’t
seem to exist on my computer.

I’m sorry I’m not very helpful in resolving the issue. I’m
new
to
this
:/

Thank you so much!

On Apr 6, 2015, at 11:45 AM, Bryce van de Geijn <
[email protected]> wrote:

What is written to stdout and stderr? There might not be
an
error,
but
this could still give us some clues.

On Mon, Apr 6, 2015 at 1:00 PM, Kimberly <
[email protected]>
wrote:

The output files are empty but I receive no error
message
or
anything.
I
have no idea why my accepted_hits.quality.remap.num.gz
and
remap.fq.gz
files are empty

—
Reply to this email directly or view it on GitHub
#8.

—
Reply to this email directly or view it on GitHub <

https://github.com/bmvdgeijn/WASP/issues/8#issuecomment-90193144>.

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#8 (comment)
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from wasp.