Hi
I have an urgent question about running rMATs, I usually running rMATs after running STAR alignment with original fastq files.
However, I'm unable to find the original fastq files recently, and I need to use the bioinformatic tools to detect novel and annotated events, I'm wondering if I can use the pseudoalignments bam file from Kallisto to run rMATs? or if there are any suggestions?
Thank you!!
1 answer
No, you can't do that with kallisto's bam files. For one, kallisto (by default) doesn't map to introns which is required by rMATs.
You could probably use some exon-based/transcript-based method for differential exon usage or isoform switching. See https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html#are-there-different-approaches-to-analysis-of-alternative-splicing
Honestly though, just try to get the original FASTQ files ASAP.
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