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  • 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.

  • #2
    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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    • #3
      Thank you.

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