enormandeau / go_enrichment Goto Github PK

I am following the described workflow for my Trinity file. I want to know how to create association.tsv file which is used in step5.
I used all_annotations_transcripts.tsv which was generated in step 3, but it gave me error.

02_go_database/go-basic.obo: fmt(1.2) rel(2021-11-16) 47,155 Terms
HMS:0:00:00.357379       0 annotations READ: all_annotations_transcripts.tsv 
Study: 972 vs. Population 176407

**FATAL: NO POPULATION ITEMS SEEN IN THE ANNOTATIONS

Hi, I want download the nr database and find the nr.00.tar.gz (16G) is much bigger other nr.**.tar.gz (1G-2G) files . is there some redundancy between nr.00.tar.gz and others ? should I download all of them or just download nr.00.tar.gz ?

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

• 01_scripts/01_blast_against_swissprot.sh

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you!
-- Arman (armish/blast-patrol)

Hi, I want to use go_enrichment , but I have some question about step4 and step5.

first, in step4, how could I get the significant_ids.txt before I do Fisher tests.
second , what's the wanted_transcripts.ids and association.tsv?
third , at step3 ,I got an output file named sequence_annotation.txt . It seems don't use in step4 and step5.

could you explain these questions for me ? thank you very much.

where's p-value?

Hello and thank you very much for the go_enrichment pipeline!

I am trying to use it for part of my analysis, I got steps 01 and 02 to work by editing the code to suit my fasta files. However. I have been trying to get 03_annotate_genes.py to work for 3 days to no avail. I think the fasta iterator does not seem to do anything, no error message, no run time, nothing. At the end an empty file with "Name" "Accession" etc titles is created. I have been through the script several times and just can't figure out what could be wrong. Would you have an idea what it could be?

Thanks a lot!

Jan