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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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Flair collapse returns isoform as same as reference #262

Closed NHoang98 closed 10 months ago

NHoang98 commented 1 year ago

Hello, I'm having my very first experiment with flair for my ONT data. But while running the collapse module, I'm facing the issue when the *.isoform.gtf somehow keeps returning isoforms the same as the reference annotation. I've checked the exon boundary manually (both in genome viewer and gtf files) and didn't see the difference.

Luamau

The script was: flair collapse -g Documents/Luamau/Ref/R498.fasta -q Documents/Luamau/FLAIR2/correct/correct/Luamau.bed -r Documents/Luamau/Trim-read/*.fastq -f Documents/Luamau/Ref/R498.gtf -o Documents/Luamau/FLAIR2/collapse/Luamau_ultraII -t 16 --generate_map --stringent --isoformtss --annotation_reliant generate --check_splice --keep_intermediate --support 0.1 --filter nosubset --no_redundant best_only

Could you please explain to me what I've done that led to this problem?

Bests, Hoang

Jeltje commented 1 year ago

It may have to do with your last option --no_redundant best_only This asks flair to report only the most supported isoform, and that's probably the reference one.

Removing that should give you better results.

If this solves your issue please close this ticket.

Jeltje commented 10 months ago

Closing because no response. Please reopen if your issue was not resolved.