Question: Remove "no_feature" and "alignment_not_unique" counts before using EdgeR or Deseq2
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gravatar for cottrellka
6 months ago by
cottrellka0
cottrellka0 wrote:

This is my first time using EdgeR or DeSeq2. I used HTSeq-Count to get counts for reads aligning to CDS (this is for ribosome profiling) for each gene. I obviously have a fair number of multi-aligning reads and reads that don't align to the feature (CDS). Should I remove these before running EdgeR or Deseq2?

 

 

 

edger deseq2 • 118 views
ADD COMMENTlink modified 6 months ago by Gordon Smyth37k • written 6 months ago by cottrellka0
Answer: Remove "no_feature" and "alignment_not_unique" counts before using EdgeR or Dese
0
gravatar for Gordon Smyth
6 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

I think you will find that edgeR and DESeq2 both remove these rows of the htseq output automatically, so you don't have to do it yourself.

But htseq isn't Bioconductor software. You might consider using the Bioconductor package Rsubread instead, which has been benchmarked as faster and more accurate. Rsubread produces a matrix of counts directly as an R object, so the issue you dealing with doesn't arise.

https://www.biorxiv.org/content/early/2018/07/26/377762

ADD COMMENTlink modified 6 months ago • written 6 months ago by Gordon Smyth37k

Thanks for the input.

ADD REPLYlink written 6 months ago by cottrellka0
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