problems in accepting annotation file

[yurokohiya]

Hi,

I think I adjust the annotation file as required:

and I ran like this:
python geneext.py -g A.gtf -b all.bam" -o geneext.gtf

However, it failed. I wondered why:

[zolotarovgl]

Dear, yurokohiya.
The gene novel_gene_2317_... is missing the exons as indicated in the error message.
You can try fixing your genome with agat tool before running GeneExt using the following command:

https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gxf2gxf.html

[yurokohiya]

Hi, this problem solved, but I also met another question in another case. I prepared the .gtf annotation file, and .bam file obtained from cellranger to run the pipeline, and geneExt seemed to run smoothly: But there's nothing as the output. Then I noticed that I probably failed in creating index for .bam file, and it stuck here. I wonder what caused this problem and how can I fix it? At 2024-07-09 16:03:33, "Grygoriy Zolotarov, MD" ***@***.***> wrote: Dear, yurokohiya. The gene novel_gene_2317_... is missing the exons as indicated in the error message. You can try fixing your genome with agat tool before running GeneExt using the following command: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gxf2gxf.html — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[zolotarovgl]

Hmm, why do you think it's a problem with .bam indexing? Have you tried indexing the .bam file yourself with samtools index ? Can you list the tmp folder contents?
Usually, the source of most of such behaviour is a discrepancy between chromsomes in .bam file and gtf file - this causes bedtools commands to silently die and not easy to catch.