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Old 11-08-2013, 05:54 AM   #6
Location: USA

Join Date: Jun 2012
Posts: 23

I just realized I'm only seeing this in my smallRNA libraries (adapter removed, t/rRNA removed, size-selected for 20-25nt in sRNA Workbench).

I map the reads using bowtie (-v 0).

I generate read counts with htseq-count, then build my count table(s).

I run DESeq following along with the vignette section 3.1.

So far, every 1v1 count table I've looked (7 of the possible 15) at has called more significantly changed loci (padj < 0.05) than I get when looking at the exact same comparison using a count table that includes all 30 of my bio-reps.

The biggest 'jump' was from 76 to 372 loci for one comparison.
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