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alternative splicing analysis

I am trying to find a good software to do alternative splicing analysis for RNA-seq data. I was told that the STAR 2-pass mode would help identifying the splice variants. and then rMAT can be used for statistical analysis. another person suggested Varscan2 for alternatve splicing. Which one is better?
Also, please suggest alternative splicing analysis softwares for RNA-seq data.

aligner rna-seq sequencing rna pipeline
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updated by jaro.slamecka jaro.slamecka • written by ams2021 • ams2021

2 answers

Give LeafCutter a look. It works with STAR in 2-pass mode as one of the supported tools for alignment.

https://davidaknowles.github.io/leafcutter/index.html

publication:

https://doi.org/10.1038/s41588-017-0004-9

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written by jaro.slamecka jaro.slamecka

Hello Jaro, Excuse me Did you find a pipelin for your analysis? I am looking for the same information as you asked.

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written by Jwan • Jwan

Hey Jwan, not sure if you meant to ask the OP instead but in my experience, the STAR 2-pass and LeafCutter pipeline works pretty well, it needed a few small tweaks but that's it.

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written by jaro.slamecka jaro.slamecka

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