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Automatically exported from code.google.com/p/align2rawsignal
Add option to produce stranded and unstranded signal output
Original issue reported on code.google.com by [email protected]
on 29 Dec 2010 at 7:26
What is the expected output? What do you see instead?
Wiggle File. Nothing is generated.
What version of the product are you using? On what operating system?
Align2rawsignal-2.0 on Linux
Please provide any additional information below.
Command I tried - align2rawsignal -i=file_bowtie.bam -s=~/genome/mm9
-u=~/bin/globalmap_k20tok54 -o=~/data/align2rawsignal.out -of=wig -m=20
Original issue reported on code.google.com by [email protected]
on 29 Apr 2013 at 3:50
What steps will reproduce the problem?
- Occurs with any BAM file, or with multiple
- install-dir/align2rawsignal/bin/align2rawsignal -v=out.log -i=1.bam -s=install-dir/Software/align2rawsignal/seq/mm9/ -u=install-dir/Software/align2rawsignal/umap/mm9/globalmap_k20tok54/ -o=output.wig -of=wig
What is the expected output? What do you see instead?
An output wig file was expected.
Out.log was created and this was sent to stdout.
??? Error using ==> readBAM at 68
Unable to extract data from BAM file:
Error in ==> preprocessAlignData at 78
Error in ==> align2rawsignalMain at 66
Error in ==> align2rawsignal at 119
Error using ==> readBAM at 68
Unable to extract data from BAM file:
What version of the product are you using? On what operating system?
Version 2.0
Ubuntu
Please provide any additional information below.
After looking through src, I found that the awk command on lines 60 and 64 of readBAM.m seemed to lead to the error in question. When manually run with the BAM files certain parts of the line 60 and 64 pipeline worked, but the awk command did not. When the "and($2,16)" command was replaced by "$2" it seemed to work in theory and no "error file" was created to stop the program in line 68 (though a file containing the extracted BAM was). I would like to know what the "and" function within awk is meant to do, I cannot find it anywhere in awk documentation. Do you know what may be causing this problem?
Original issue reported on code.google.com by [email protected]
on 20 Nov 2014 at 9:47
Along with fold change allow for poisson p-value output
Original issue reported on code.google.com by [email protected]
on 29 Dec 2010 at 7:25
Stack filter similar to that used in SPP
Original issue reported on code.google.com by [email protected]
on 29 Dec 2010 at 7:24
Prefilter reads wrt blacklist (especially chrM)
Original issue reported on code.google.com by [email protected]
on 29 Dec 2010 at 7:27
Instead of rectangular kernel use smoother kernel
Original issue reported on code.google.com by [email protected]
on 29 Dec 2010 at 7:24
What steps will reproduce the problem?
1.
2.
3.
What is the expected output? What do you see instead?
What version of the product are you using? On what operating system?
I am using align2rawsignal/2.0 on Ubuntu
Please provide any additional information below.
I have longer reads than 54bp, and cannot find the suitable mapability track.
Is it possible to please update that for longer reads as well?
Original issue reported on code.google.com by [email protected]
on 17 Jul 2015 at 11:44
What is the expected output? What do you see instead?
bedgraphs. nothing...
What version of the product are you using? On what operating system?
align2rawsignal 2.0 on linux
Please provide any additional information below.
./align2rawsignal/bin/align2rawsignal -i=../file.bam -s=encodeHg19Male
-u=mappabilityTracks/H.sapiens/globalmap_k20tok54 -l=185 -of=bg -mm=4
-o=test.bedGraph
??? Too many outputs requested. Most likely cause is missing [] around
left hand side that has a comma separated list expansion.
Error in ==> initializeUmapParams at 56
Error in ==> align2rawsignalMain at 43
Error in ==> align2rawsignal at 119
Too many outputs requested. Most likely cause is missing [] around
left hand side that has a comma separated list expansion.
MATLAB:TooManyOutputsDueToMissingBraces
Original issue reported on code.google.com by [email protected]
on 7 Oct 2013 at 10:16
Current chromosome names have to start with chr and require exact naming
schemes between seq/ umap/ and alignment files. Rather allow user to provide a
mapping file for chromosome names between the 3 entities.
Original issue reported on code.google.com by [email protected]
on 8 Sep 2012 at 1:36
What steps will reproduce the problem?
Just trying to run align2rawsignal and getting this error message every time:
/net/gerstein/as2665/Pipelines/align2rawsignal/bin/align2rawsignal -i=test.bam
-s=/net/gerstein/as2665/ChromSeq/mm9/
-u=/net/gerstein/as2665/Pipelines/globalmap_k20tok54/ -o=test.wig -of=wig -v=log
What is the expected output? What do you see instead?
wig format
Program quits with the following message:
Too many outputs requested. Most likely cause is missing [] around
left hand side that has a comma separated list expansion.
MATLAB:TooManyOutputsDueToMissingBraces
What version of the product are you using? On what operating system?
Version 2.0
OS: Red Hat Enterprise Linux Server release 6.2 (Santiago)
Please provide any additional information below.
I have not been able to run the program so far. But I saw something similar in
issue number 9. I am giving the whole path to the program but still have the
same issue.
Original issue reported on code.google.com by [email protected]
on 2 Oct 2014 at 3:32
Currently the code cannot work without a mappability track. Allow a user to
provide an empty umap directory where the code will generate a fake mappability
track allowing all bases.
Original issue reported on code.google.com by [email protected]
on 8 Sep 2012 at 1:38
What steps will reproduce the problem?
1. Generate a SAM file with "*" string at 10th column.
2. Convert it to BAM and run align2rawsignal.
3. It fails with error message "Read lengths not supported by mappability data"
since it thinks that all reads are 1bp in length. However, read lengths are
specified in sixth column of the SAM file as "36M".
bamToBed, on the other hand, can convert this kind of BAM files to correct BED
files.
What is the expected output? What do you see instead?
It should process the file and generate output.
What version of the product are you using? On what operating system?
Latest SVN trunk on Linux x86_64.
The following bed-to-bam conversion method given in phantompeakqualtools
homepage[1] also gives incorrect results since it considers only sequence
field, too:
samtools view -F 0x0204 -o - <bamFile> | awk 'BEGIN{OFS="\t"}{if (and($2,16) >
0) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print
$3,($4-1),($4-1+length($10)),"N","1000","+"} }' | gzip -c >
<gzip_TagAlignFileName>
Sample SAM file is attached.
[1] https://code.google.com/p/phantompeakqualtools/
Original issue reported on code.google.com by [email protected]
on 31 Jul 2014 at 11:28
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