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  • SamCurt
    Member
    • May 2010
    • 40
    #1

    Alternate Contigs and Gene expression profiling

    Currently I do my RNAseq analyses using the primary-assembly-only version of GRCh/GRCm38 from GENCODE, and their annotations thereof.

    Upon reading Broad's recent guide on alt-contig-aware variant calling in GATK, I wonder anyone have an idea on whether using the alternate contigs (but staying in the same assembly version) would affect gene expression profiling results?
    Tags: None
    • dpryan
      Devon Ryan
      • Jul 2011
      • 3478
      #2
      There aren't any alt-aware RNAseq aligners (that I know of), so including the alt-contigs will deflate counts of genes on those contigs.

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