Why is there a big difference between kallisto and cellranger count result？ - Githubissues

pachterlab / kallisto

Near-optimal RNA-Seq quantification

https://pachterlab.github.io/kallisto

BSD 2-Clause "Simplified" License

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Why is there a big difference between kallisto and cellranger count result？ #376

Open aizhimin opened 1 year ago

aizhimin commented 1 year ago

Why is there a big difference between kallisto and cellranger count result？

sample： https://www.ncbi.nlm.nih.gov/sra/SRR8315735

kallisto:

cellranger:

Yenaled commented 1 year ago

Can't really tell unless I see the commands used and how the index was generated.