Alternate Contigs and Gene expression profiling

SamCurt

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Join Date: May 2010

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Alternate Contigs and Gene expression profiling

08-19-2016, 12:43 PM

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?
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dpryan

Devon Ryan

Join Date: Jul 2011

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08-19-2016, 08:36 PM

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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Alternate Contigs and Gene expression profiling

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