Bioconductor Rawcounts

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DESeq2 TPM rawcounts StringTie

updated 2.3 years ago by Michael Love 43k • written 2.3 years ago by snijesh ▴ 200

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Normalisedcounts Rawcounts Ht-SeqRNAData BatchEffect

2.8 years ago Ety • 0

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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…

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Comment: ANOVA like approach of edgeR

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