search

wyguo / ThreeDRNAseq

A pipeline for differential expression and differential alternative splicing analysis
https://github.com/wyguo/ThreeDRNAseq
GNU General Public License v3.0
60 stars 27 forks source link

running 3DRNAseq at gene level #23

Open Shukla04 opened 4 years ago

Shukla04 commented 4 years ago

Hello, I have a question. Can the app be used to find DEGs in cases where transcript isoforms are not know. I am working with an organisms where only one isoform is known for one gene. I tried to run the app but crashes at 3DAnalysis step. And I see the following error: Warning: Error in diffSplice: No genes with more than one exon 79: stop 78: diffSplice 77: limma.pipeline [R/pipeline.R#268] 73: observeEventHandler [source/server/server_ddd.R#503] 2: shiny::runApp 1: run3DApp [R/run3DApp.R#16]

Is there a way to still use the app or I have to use another software?

Thank you

wyguo commented 4 years ago

Hi, The 3D RNA-seq App currently does not work for only gene level analysis. To do this, you need to use commad lines of 3D RNA-seq analysis at gene level (just skip the transcript level analysis) and then do a bit of summary by yourself. The user manual of command line can be find in: https://github.com/wyguo/ThreeDRNAseq/blob/master/vignettes/user_manuals/3D_RNA-seq_command_line_user_manual.md

Shukla04 commented 4 years ago

Thank you. Will try!!