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!
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written
by
Aynur •
2 answers
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
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
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