RNA-seq: Drosophila`s .GFF (assembly 6/6.32) gives errors in the HTseq tool

usegalaxy.org support
1

Dear support team at GALAXY,

I am trying to perform a RNA-seq analysis for D. melanogaster. I did the mapping with Bowtie2, using the genome assembly: dmelo_r6.32 and all were fine, nice mapping stats etc. Then, I tried to generate the necessary matrices for the DEseq tool via using the tool HTseq:

When I used the corresponding .GFF ( dmel-all-r6.32.gff.gz ) for this particular assembly, I got the error below:
image
When I used the .GFF for the assembly 6 from the NCBI, then I got the error below:

image
image770×272 38.4 KB

Any input on how to overcome this obstacle in my analysis will be highly appreciated.

Manolis

2

Hi @Manolis1,
could you share the history with me? I’ll have a look. My email is: Screenshot from 2022-04-03 16-52-09

Regards

3

Hi,

Thank you very much for your response and my apologies for my delayed answer.
I have resolved the issue by using a different (an older) assembly genome file and its corresponding GFF.

Greetings,

Manolis

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