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GuyTeichman / RNAlysis

Analyze your RNA sequencing data without writing a single line of code
https://guyteichman.github.io/RNAlysis/
MIT License
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Feature Request: differential expression of transcripts #41

Open santataRU opened 2 weeks ago

santataRU commented 2 weeks ago

Is your feature request related to a problem?

Is there a way to do differential expression of transcripts (e.g. similar to DEseq2 but for transcripts) with RNAlysis?

Describe the solution you'd like

A pipeline for transcript quantification and differential expression analysis between RNA-seq data from control and treatment groups.

Describe alternatives you've considered

Something similar to DESeq2 for genes, but specifically for transcripts in this case.

Additional context

No response

Which version of RNAlysis do you typically use?

No response

GuyTeichman commented 2 weeks ago

Hi santataRU,

You should be able to run differential expression of transcripts using DESeq2 (basically treating individual transcripts as genes), and quantify transcript-level expression using Kallisto.

Hopefully in the next RNAlysis version I will implement support for differential splicing analysis usinhg limma-voom.

Best, Guy.