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Published 20 hours ago • verified publisher icon pachterlab

RNA isoform/alternative splicing analysis

Open grimwoo opened this issue 4 years ago • 5 comments

Hi, Kallisto/BUSTools was recommended by Seurat to perform RNA isoform/alternative splicing analysis. However, I didn't find the related workflow and found nothing in GitHub with the key word "isoform". This may due to my poor understanding of this package. Coud anyone help me ?

grimwoo avatar Apr 13 '20 06:04 grimwoo

What is the datatype, 3' or full length (ie Smart-seq?)

sbooeshaghi avatar Apr 13 '20 18:04 sbooeshaghi

@sbooeshaghi Thank you for the early reply. The datatype is 10x single cell RNA seq ( 3').

grimwoo avatar Apr 15 '20 03:04 grimwoo

Hi, was just wondering if there's been any update to this question? I'm interested in alternative splicing analysis as well.

LuoJulia avatar May 26 '20 20:05 LuoJulia

Dear Devs

I am also interested in alternative splicing analysis (10X with hashtag oligo data) :-)

tstannius avatar Sep 16 '20 16:09 tstannius

@sbooeshaghi Hello, is there any update on the Differential expression with equivalence classes in TCC matrix (coming soon) using the kb-python ?

gadepallivs avatar Mar 30 '23 14:03 gadepallivs