Bioconductor Total RNA

Showing : total RNA • reset

6

votes

6

replies

6.8k

views

RNA-seq featureCounts total RNA

updated 2.1 years ago by snijesh ▴ 200 • written 6.5 years ago by inah ▴ 10

1 result • Page 1 of 1

Recent ...

Replies

Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10

@gordonsmyth I am exploring workflows for differential transcript expression analysis and have been using the nfcore rnasplice pipeline, w…

Answer: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k

I haven't used nf-core but, from browsing through their documentation, they didn't seem to have any pipeline for differential transcript ex…

Comment: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k

The poster needs to run Salmon with `--numGibbsSamples=50`. I suspect that nf-core just won't do that, so Salmon needs to be run directly.

Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.6k

Probably nf-core did not run with bootstrap/gibbs replicates. Check the code. See salmon docs on how to turn that on.

Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10

@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…

Votes

Comment: ANOVA like approach of edgeR

Awards • All

Popular Question to Marek Gierlinski ▴ 30

Scholar to Gordon Smyth 52k

Popular Question to mohammedtoufiq91 ▴ 10

Popular Question to Hans-Ulrich Klein ▴ 330