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Recent Replies
Comment: High duplicate BUSCOs after annotation but not assembly
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Thanks for the quick response, Juke. I'll look into AGAT, although I think I've had problems with both Singularity and Docker.
What exactl…
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I used it in the RSEM pipeline where I also have STAR as an option. Just want to confirm using bowtie2 in RSEM pipeline. Thanks so much!
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Technically, it's perfectly fine if you use bowtie2+RSEM (which doesn't use genome alignment).
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Agreed, and also, there are plenty of publications using it and its being mainteined very frequently, with the last update beign from Jan 1…
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Hi, I suppose you used stringtie for the assembly of the trasncripts, correct?
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It will most likely not be possible to load these data into memory, so this will require some on-disk representation, see e.g. http://bioco…
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`cdsBy()` and `exonBy()` return similar output, with one being exon specific and the other exon specific. Other than the titles of the colu…
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Sounds like a fragmented annotation. You might check what is going on to the BUSCO genes from your assembly to the annotation using agat_sp…
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It is non random but there is no biological meaning in this
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