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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

[Enhancement] #35

Open aru1593 opened 2 years ago

aru1593 commented 2 years ago

The loading transcriptome mapping file is taking forever. I have uploaded a gtf file and since two days it shows loading transcript gene mapping. My internet may be slow but this is still taking a lot. today is the second day I have kept it on loading. Screenshot (6)

Screenshot (6)

wyguo commented 2 years ago

Hi Gene-transcript association information in the Gtf or fasta file is often incomplete or massed up by other information, it depends on how the gtf or fasta file is created. In your case, it seems that the gtf file has issues providing the information. I would recommend making a gene-transcript association csv file as the input. Best

aru1593 commented 2 years ago

Hi, Now I made a csv file of it. I started it 2 hourd ago. It is still coming loading transcript gene mapping.... Does csv file also take a long while ?

On Tue, 4 Oct 2022, 15:54 Wenbin Guo, @.***> wrote:

Hi Gene-transcript association information in the Gtf or fasta file is often incomplete or massed up by other information, it depends on how the gtf or fasta file is created. In your case, it seems that the gtf file has issues providing the information. I would recommend making a gene-transcript association csv file as the input. Best

— Reply to this email directly, view it on GitHub https://github.com/wyguo/ThreeDRNAseq/issues/35#issuecomment-1266732265, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3NAJCXIX5UMZ5J6KOPR72DWBQAUZANCNFSM6AAAAAAQ335DWQ . You are receiving this because you authored the thread.Message ID: @.***>

wyguo commented 2 years ago

Hi, I should only take a few seconds. Would you mind sending me the csv file? I can take a look. My email: wenbin.guo@hutton.ac.uk