Hi Everybody,

I 44 samples and >76000 transcripts in my RNA Seq data which was counted using FeatureCounts.

I'd like to reduce the number of transcripts by filtering out the transcripts in which 80% of the samples (35 samples) have >10 reads.

Can anyone suggest how I may do so?

Thanx.

carol

hi Carol,

In DESeq2, filtering of low count reads is handled automatically in the results() step. This uses software from the genefilter package on Bioconductor, to optimize the number of adjusted p-values less than a given value, say 0.1. We discuss the logic behind this here in the Independent Filtering section of the new paper:

http://genomebiology.com/2014/15/12/550

So you can either switch to DESeq2 (recommended) and this is taken care of for you, or you can use the genefilter package with DESeq.

Note: you should use gene counts, not transcript/isoform counts with DESeq or DESeq2. Search the support site for "DESeq transcript-level" for many discussion on why this is the case.

If you absolutely need to get the rows that satisfy the above criterion, it would be:

use = apply(counts(dds), 1, function(k) mean(k > 10)) > 0.8

Thank you Michael!