Workflow/pipeline for detecting isoforms/alternative splicing

Question

[Aynur]

Hello, I am doing a DEG analysis using the STAR-HTSeq-DESeq2 pipeline on mouse RNA-seq. I am also interested to detect isoform or alternative splices. I read this post a tool for alternative splicing. But it seems to be an old post, and I also checked MATS, but I have a hard time installing those dependencies to my cloud. So, can you recommend me any other tool for isoform/ alternative splicing detection following my DEG pipeline? Any tools for GO and pathway analysis for the mouse genes?

Thank you!

[ATpoint]

You can install most software via package managers such as conda which take care of all dependencies.

Answer 1

[antonioggsousa]

Hi,

Not familiar with differential isoform usage, but this vignette seems to be a good starting point: http://bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html

Regarding GO analysis, there are several tools out there. One is topGO R package: https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf

I hope this helps,

António

Answer 2

[Nathan Salomonis]

Try AltAnalyze which has a GUI and hence, dependencies are less of an issue (good to still install R and hopach in R). http://www.altanalyze.org

The software can be run by GUI or command-line, enables direct analysis of FASTQ files (modification of Kallisto for pseudo-alignment) to derive BAM files and automates gene expression and splicing differential comparative analyses (with plots, including automatic SashimiPlots). Also compatible with a directory of BAM files. If you have hg38 data, contact us to get access to the newer database.

Nathan