updated 4.8 years ago by
James W. MacDonald
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written 4.8 years ago by
Marco Blanchette
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Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
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Hi Gordon,
Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be.
Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
by
Michael Love
43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed".
For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts
by
Gordon Smyth
52k
The behavior that you have documented is expected and is explained in the featureCounts documentation.
The first thing to understand is th…
Answer: Feature Counts -R XS Read Assignment Tag
by
Gordon Smyth
52k
No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…
Comment: Margins for gene_set_enrichment_plot
by
Leonardo Collado Torres
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1.1k
Thanks! This one might be worth remaking with `ComplexHeatmap`. Similar to https://github.com/LieberInstitute/spatialLIBD/pull/91 that was …
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