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wyguo / ThreeDRNAseq

A pipeline for differential expression and differential alternative splicing analysis
https://github.com/wyguo/ThreeDRNAseq
GNU General Public License v3.0
61 stars 26 forks source link

Cannot load csv or gtf only .fasta[Help] #27

Open jason2389 opened 3 years ago

jason2389 commented 3 years ago

Thanks for using our 3D RNA-seq App.

Hi! Thanks for creating this great App. I have a problem with loading the geneid. The App only manages to get them from the .fast file. While if I give it a .gtf or .csv is gets stuck on loading and the program crashes. I tried both on my PC with R and on the web-based App. What could be the problem? Furthermore, the App tells me there are only 34 raw genes, whereas when I look into the Quant.sf files several genes have counted reads. I am using Arabidopsis fast and gtf file downloaded from Araport11.

Thank you for your help

wyguo commented 3 years ago

Dear User, Many thanks for using our 3D RNA-seq App.

It is better to use csv format to tell the App the transcript and gene assocation, because the descritpion lines of gtf or fasta often have incomplete or overmuch information. This may lead to problems of uploading the data to the App. I suppose the format of your csv file is incorrect. You can follow the user manual and the example dataset to check the format: https://github.com/wyguo/ThreeDRNAseq/blob/master/vignettes/user_manuals/3D_RNA-seq_App_manual.md#input-files. If you still have problem, could you please enclose a screenshot of your csv file? I can take a look to figure out the issue. All the best.