DEXSeq on FeatureCounts output
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Vivek.b ▴ 100
Last seen 3.4 years ago

Dear DEXSeq and FeatureCounts team

I was wondering if it is possible to better integrate DEXSeq with featureCounts (either the RSubread or the command line version) output, so that users don't have to modify the FeatureCounts output to convert into DEXSeq acceptable format. I have been doing this by adding Exon IDs (E1,E2..) to the gene names followed by  inputting it to DEXSeqDataSet command. However still I found that some of the plots didn't work properly (probably that's not the best way to do it). It would be great to have something like DEXSeqDataSetFromFeatureCounts function, or probably getting RSubread output in a SummarizedExperiment format. However, I would appreciate any advice on this issue.


dexseq featurecounts • 3.1k views
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Hi Vivek.b, 

Would be happy to implement this integration in DEXSeq. Do you have a prototype code from the featureCounts part? Does it follow the same "counting rules" described in the DEXSeq manuscript/vignette?


Entering edit mode

Hi Alejandro

Thanks for your reply (and sorry for my late reply). I had to make a couple of changes to make it work:

  • DEXSeq-flattened GFF converted to GTF for featurecounts.
  • Adding exon IDs to featurecounts output.
  • Made a DEXSeqDataSetFromFeatureCounts function to read the converted output into dexSeq.

After running DEXSeq, the output from featureCounts (if we also count reads overlapping more than one feature), is very similar to that from DEXSeq_count. Just that featureCounts is much faster. 

Now I can also visualize my output properly using plotDEXSeq and DEXSeqHTML functions. So things are working for me.

I have put my scripts on Github here.. I hope this can be integrated into DEXSeq.


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