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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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A false transcript cooordinate? #182

Closed OlgaVT closed 2 years ago

OlgaVT commented 2 years ago

Hi,

after flair collapse a transcript seems to have wrong coordinates. flair reports 2 FLAIR transcript 65056416 65084522 . + . gene_id "ENSG00000011523"; transcript_id "ENST00000377990";

But in the Ensembl 99 annotation that I used the coordinates are: 2 ensembl_havana transcript 65056416 65087004 . + . gene_id "ENSG00000011523"; gene_version "14"; transcript_id "ENST00000377990"; transcript_version "7";

The command lines I used:

python flair.py align -r my.fastq -g Homo_sapiens.GRCh38.dna.primary_assembly.fa python flair.py correct -q flair.aligned.bed -g Homo_sapiens.GRCh38.dna.primary_assembly.fa -f Homo_sapiens.GRCh38.99.gtf python flair.py collapse -r my.fastq -g Homo_sapiens.GRCh38.dna.primary_assembly.fa -q flair_all_corrected.bed -f Homo_sapiens.GRCh38.99.gtf

Do you know what might be wrong?

Thank you!

Jeltje commented 2 years ago

Hi OlgaVT,

Apologies for the delay in replying. I believe the underlying code for this step has been updated since your question, would you mind trying your run with the current version? Please reopen this ticket if you have the same issue.