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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
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[Help] #1

Open amrsc23 opened 4 years ago

amrsc23 commented 4 years ago

Hi,

I am new to the 3D RNA-seq App and when I upload all the input files (3) the screen becomes grey. Is it loading/in queue or is it someting about the files?

Thank you, Ana

wyguo commented 4 years ago

Hi Ana, Thanks for using our App. Could you please provided more details about your input file (3) (1) Which tool you used for transcritp quantification to generate input file (3), salmon or kallisto?
(2) If you use kallisto for quantification, do you have abundance.tsv files in your input file folder? (3) How big is your input file (3)? If your dataset is extremely big, you may get problem. It would be better if you can attach a screenshot of your input file 3 and the content in its sub-folders.

PS: You can double check if your input files follow the format in the user manual:https://github.com/wyguo/ThreeDRNAseq/blob/master/vignettes/user_manuals/3D_RNA-seq_App_manual.md#input-files. You can also format your input files according to the Arabidpsis example dataset: https://www.dropbox.com/s/8vwuz6u2yl7v9qx/3D%20RNA-seq%20App%20example%20data.zip?dl=0.

Best, Wenbin