TopHat v2.0.13 generates SAM files with few alignment records having empty QUAL field

[srikant_verma]

Hi all,

I have obsereved that a couple of alignment records as generated by TopHat has empty QUAL field (11th column) in SAM file.
This results the following error while converting this SAM file to BAM using samtools 1.0 (view):
[W::sam_read] parse error at line 83974818
[main_samview] truncated file.

It would be great if you let me know what could be the reason for the empty QUAL field.

Thanks,
Srikant

[blancha]

First, I would start by offering my standard advice that you should upgrade to the latest version of the programs before reporting any potential bug.

Second, your post is confusing. TopHat directly outputs BAM files. How come you are using samtools view to convert a SAM file supposedly outputted by TopHat to a BAM file?

[srikant_verma]

Thanks blancha for your suggestion.

According to the release related information available at https://ccb.jhu.edu/software/tophat/index.shtml, the problem mentioned above was solved/tried to solve in release TopHat 2.0.1 maintenance release 5/17/2012 and TopHat 2.0.7 release 1/23/2013. So I thought there could be other reason for the observation which I do not know.
Regarding your second query, there is the option '--no-convert-bam' in tophat which generates <output_dir>/accepted_hit.sam. I use this SAM file for some other purpose (using custom perl script). Anyway, the SAM file then can be converted to BAM using samtools view, and that can be used in down-stream analysis.

Again, thanks for your suggestion. I will use latest tophat and post the result.