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RikyJKD 07-11-2016 05:59 AM

RSEM bam question
Hi, I used RSEM with STAR. I noticed that in the RNAME field of the BAM (3rd filed) , where usually had e.g chr1 now I have the name of the isoform. With this BAM I can not find the chr but I need this information.
Is it normal to have this kind of BAM?
How can I solve this problem?
Thank you.

dpryan 07-12-2016 12:48 AM

RSEM needs alignments against the transcriptome, so it'd be a big problem if you had chromosomal coordinates. So this is expected (required even), it's not a problem.

RikyJKD 07-12-2016 01:53 AM

Thank you.

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