doaneas / align2rawsignal Goto Github PK

Add option to produce stranded and unstranded signal output

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

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?

Along with fold change allow for poisson p-value output

Stack filter similar to that used in SPP

Prefilter reads wrt blacklist (especially chrM)

Instead of rectangular kernel use smoother kernel

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?

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

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.

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. 

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.

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/