Import Error with annotating Deseq2 results

1

Hello, I am very new to galaxy and attempting to use Deseq 2 on my first data set. I ran deseq2 with 6 files (3 treated 3 untreated). I got a successful result, however, I then attempted to use the annotating Deseq2 result file tool and I keep getting the error:
“ImportError: cannot import name ‘UnknownSeq’ from ‘Bio.Seq’ (/home/galaxy/database/dependencies/_conda/envs/mulled-v1-61ba501081daf9921383c1402c51e68d5421ca2253eaf7867e6d4de3e09b2263/lib/python3.12/site-packages/Bio/Seq.py”

I am using the hg38 file to compare, and I have used the UCSC and NCBI version, however both ways I continue to get this error. Thank you so much for your time and any insight you can provide on this issue would be much appreciated.

2

Hi @Priya_Das
I am not familiar with this tool, but maybe check if the selected values are present in the annotation file (column 9, attributes).
If you share the history, I can have a look.
Kind regards,
Igor

3

@igor Here is the history. Thank you for your help.

http://cancer-bmv50c3.osumc.edu:8080/u/das31/h/copy-of-copy-of-unnamed-history

4

The GTF file of hg38 that I am using has both exon and mRNA in the 9th column. Would this affect it?

5

Hi @Priya_Das
I cannot connect to the server.
Maybe try the tool on any public Galaxy server, such as usegalaxy.org
It is OK to have accounts on different Galaxy servers.
Kind regards,
Igor

6

I will attempt that. Thank you for your help @igor !