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Old 07-11-2016, 04:59 AM   #1
RikyJKD
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Location: Torino

Join Date: Jul 2014
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Default 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.
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Old 07-11-2016, 11:48 PM   #2
dpryan
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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.
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Old 07-12-2016, 12:53 AM   #3
RikyJKD
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Thank you.
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