Question: Workflow/pipeline for detecting isoforms/alternative splicing
0
gravatar for Aynur
8 weeks ago by
Aynur40
Aynur40 wrote:

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!

sequencing rna-seq next-gen R • 189 views
ADD COMMENTlink modified 7 weeks ago by Nathan Salomonis70 • written 8 weeks ago by Aynur40
1

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

ADD REPLYlink written 7 weeks ago by ATpoint40k
2
gravatar for antonioggsousa
8 weeks ago by
antonioggsousa1.5k
antonioggsousa1.5k wrote:

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

ADD COMMENTlink written 8 weeks ago by antonioggsousa1.5k
1
gravatar for Nathan Salomonis
7 weeks ago by
Cincinnati Children's Hospital Medical Center
Nathan Salomonis70 wrote:

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

ADD COMMENTlink written 7 weeks ago by Nathan Salomonis70
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