search

TRISTAN-ORF / RiboTIE

Scripts and instructions to apply RiboTIE on Ribo-seq data
MIT License
10 stars 0 forks source link

AssertionError: No transcripts in training data #10

Closed DanielAldas closed 4 months ago

DanielAldas commented 4 months ago

I am having a new problem now. I got the following error during finetuning:

Screenshot 2024-05-24 at 3 49 55 PM

I don't know what the cause could be this time. Thanks!

jdcla commented 4 months ago

Hey Daniel, Thanks for the feedback. These reports help me fix up some functionalities I hadn't thought of before. The problem here is that the pretrained model has different chromsome names than the assembly used by you. (1,2,3,4) vs (chr1, chr2, chr3, ...). The tool searches for transcripts on (1).

I'll have to create some library that automatically detects and recognizes multiple variants of the same chromosome names. I'll get to this next week. A quick hack would be to rename your main chromosomes in the gtf and fa files if you'd want a solution ASAP.

jdcla commented 4 months ago

Actually, that was bad advice, as that might give complications with the alignment in the bam.

A hack would be to copy the pre trained model weights and configuration file from the package (transcript_transformer/pre trained/ribotie/...) and alter the chromosome names in the yaml file to the ones of your assembly.

You can reference to this edited yaml.

Otherwise, I'll check this next week so if you're not in a hurry this will work soon

DanielAldas commented 4 months ago

Thanks for your advice, I am glad I'm being helpful! I will wait for you to upload the update as I am not in a hurry to run it

jdcla commented 4 months ago

This should be fixed in the latest release of transcript-transformer (v0.8.4)