Please suggest tool for splice variant identification from RNAseq data.? MAJIQ is one option. Any other suggestions?
MAJIQ, r MATS, MISO are widely used.
Splice-AI has been recently developed by Illumina for identification of splice variants affected by point mutations.
"Best" is highly subjective. It's all about the False Discovery Rate after you validate the differential splice predictions by RT-PCR and qPCR.
I didn't hear or use those proposed by others. My recommendation would be:
- CuffDiff
- SGSeq (R package going straight from sam/bam files)
- IsoformSwitchAnalyzeR (R package that parces parses cufflinks/cuffdiff output and others).
All of those have reasonably well written vignettes or manuals.
There's a lot of good info about alternative splicing analysis in this post: https://www.biostars.org/p/65617/
DiffSplice is another interesting one that I don't think has been mentioned.
Hi,
I am facing a problem with C++ 11 Compiler and HTSlib library setup for MAJIQ installation. If someone has worked with MAJIQ installation, please help me.
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