Realigning Tophat files with STAR

[Darryl Nousome]

Hi all,

I currently have Tophat aligned files (no original fastq), both the aligned and unmapped files, and wanted to generate paired fastq files to realign the files with STAR.

Do you think I should try to merge the aligned and unmapped bams and then try to convert to fastq?

I have a feeling that might not be correct because it would insert potential reads with no mate into the fastq files. Otherwise I'm a little stuck as to what to do with the unmapped file.

Thanks for any help!
Darryl

[Alexander Dobin]

Hi Darryl,

what software are you using to convert BAMs into FASTQ. I have had good experience with picard SamToFastq, it takes good care of reporting BAM formatting problems.

I would make separate transformations for mapped and unmapped, check the FASTQ consistencies for both, and then merge the FASTQs.

Cheers

Alex

[Darryl Nousome]

I tried using bamUtil which seemed to do the trick in removing alignments that were not paired correctly when splitting the original file apart.

Thanks for your help!