rsem-sam-validator

[Kerry Deutsch]

Hello -

I'm looking for some guidance on how to get my bam files validated.

I have several lanes' worth of RNA-Seq data that I aligned with STAR and generated the transcriptome-aligned bam files.  I then merged those into a single transcriptome-aligned bam for the sample.  

I ran convert-sam-for-rsem on that final bam file, and the conversion finishes successfully, but the subsequent rsem-sam-validator fails with "The two mates of paired-end read XXXXX are marked as both mate 1 or both mate2!"

I guess the error is fairly self-explanatory, but I'm not sure how to go about fixing it so that I can proceed with rsem analysis.

Suggestions for me?

Thanks!

Kerry

[Bo Li]

Hi Kerry,

You should first check why read XXXXX has two mates with both mate1 and
mate2 flags marked. In theory, STAR should not mark one read as both
mates.

Hope it helps,
Bo

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