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Comment: nightmare to make custom txdb for genomes from ToxoDB
by
rohitsatyam102
▴ 20
Hi Herve As I mentioned, for parasites we rely on VEuPathDB databases (such as ToxoDB here: https://toxodb.org/toxo/app/downloads) which p…
Comment: nightmare to make custom txdb for genomes from ToxoDB
by
Hervé Pagès
16k
`keepStandardChromosomes()` is not smart enough to know what to keep for this assembly. Note that what `keepStandardChromosomes()` means by…
Comment: nightmare to make custom txdb for genomes from ToxoDB
by
James W. MacDonald
67k
Thanks Hervé! Very helpful. However, I believe that `keepStandardChromosomes` gets called by `gDNAx`, and it appears not to work correctly.…
Answer: nightmare to make custom txdb for genomes from ToxoDB
by
Hervé Pagès
16k
Is this for genome assembly TGA4? https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006565.2/ If that's the case then: ``` library(t…
Answer: nightmare to make custom txdb for genomes from ToxoDB
by
James W. MacDonald
67k
Your post title is misleading. You have no problem whatsoever generating the `TxDb`, the problem is using it with `gDNAx`, which attempts t…
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Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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