Is it possible to use pseudoalignments.bam to run rMATs?

Question

[Lillian]

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!!

Answer 1

[dsull]

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.