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Comment: Kallisto to tximport to deseq2
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bioinfo
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Thank you so much for replying. Would you do the paste instead of tximport?
When I use biomart I specify the version I want to use to make …
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I would always do either gene_id or `paste(gene_id, gene_name, sep = "_")` because gene_name has duplicates, which can cause conflicts. Gen…
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Without further details I would recommend against doing unreplicated experiments as replication is key for any meaningful pairwise statisti…
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The background should be the set of all genes that are common to both tissues. The foreground is the set of "significant" genes (e.g., base…
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Hi,
Thank you for your comment.
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Ok, I finally find the solution. I would like to share with you guys:
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If you want to detect differential splicing using edgeR with Salmon output, then you should do DTU instead of DEU, see:
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Yeah, it's a good solution I've tried. The only problem is that the SplitFasta() process has to be finished before it starts, otherwise it …
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Providing each exon as an individual transcript will throw off pseudoalignment-type algorithms which assume that each read originated from …
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Can you set the following variable and see if that helps.
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Thank you. It is working now with:
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I had a quick look and though it is feasible to change files (and specifically feature names) such that the files correspond to each other …
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what I expected:
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