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Comment: What type of counts data to import for performing Isoform analysis in edgeR
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mohammedtoufiq91
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@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
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ATpoint
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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
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mohammedtoufiq91
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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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