[BUG] IndexError: list index out of range

[YIGUIz]

Problem description

I have loaded the SQANTI3.env conda environment

The same question have been reported in https://github.com/ConesaLab/SQANTI3/issues/329. I tried it with the new version and failed to solve this problem. Besides, the *corrected.gtf file exists and is normal.

corrected.gtf:

Code sample

Here is the command: /00bin/SQANTI3-5.2.2/sqanti3_qc.py adipose_final.gtf GCF_002263795.3_ARS-UCD2.0_genomic.gtf GCF_002263795.3_ARS-UCD2.0_genomic.fna --force_id_ignore --dir ./ --cpus 20 --short_reads test_short_reads.fofn --skipORF --report both --ignore-report-errors

No response

Error

Looking forward to your reply.

Qi

[Fabian-RY]

Hi @YIGUIz thanks for reaching us out

I can see that you're using StringTie in your screenshot. @alexpan00 and I noticed that there might be some transcripts in your data that do not have an strand value in your corrected gtf (it is a '.' instead of '+' or '-'). That is making SQANTI fail due to how BCBio_GFF parses the file.

I will work on a fix for the next release.

Thanks

[carolinamonzo]

In the meantime, you can refer to #21, #56, #142 or #235 for details and suggestions on how to solve this problem.

[YIGUIz]

Hi @YIGUIz thanks for reaching us out

I can see that you're using StringTie in your screenshot. @alexpan00 and I noticed that there might be some transcripts in your data that do not have an strand value in your corrected gtf (it is a '.' instead of '+' or '-'). That is making SQANTI fail due to how BCBio_GFF parses the file.

I will work on a fix for the next release.

Thanks

Thank you! I have other questions. If I collect hundreds and thousands of public SR RNA-seq to validate, how can I perform it quickly? Can I get Long read coverage of transcripts by SQANTI3？