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pachterlab / kallisto

Near-optimal RNA-Seq quantification
https://pachterlab.github.io/kallisto
BSD 2-Clause "Simplified" License
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Generating gene/transcript count for all samples from kallisto aligned files #354

Open SynatKeam opened 2 years ago

SynatKeam commented 2 years ago

Dear Author,

Hope you are well. Sorry to reach you again. I have completed the alignment and have some sample workflow from my colleages regarding how to generating gene/transcript count from abundance.tsv, abundance.h5 using tximport package. I find it confusing a bit with this workflow and previously found no differentially expressed genes using this workflow. kindly see link below

https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto_with_TSV_files

I am wondering whether your team has created a workflow or package that can be easily used to generate gene/transcript count for all sample in one go or you could suggest sth. I am just got stuck with it. Appreciated your kind help and input so far. Looking forward to hearing from you soon.

Kind Regards,

synat,

Yenaled commented 2 years ago

Yes, you can try sleuth for differential expression.

For help with tximport, that's not our package. Post your tximport questions on the bioconductor support forum.