A question about correct model

[anxuan-web]

Hi, I found that after running correct, the file (*_corrected.bed) became very small.

Inconsistent.bed files are very large, is this normal?

[Jeltje]

That is not normal. Can you give more information about your inputs, outputs, flair version, and exact command?

[anxuan-web]

That is not normal. Can you give more information about your inputs, outputs, flair version, and exact command?

flair correct -q GY_01_lung.bed -f ../GY.new.all.genome.gtf -g ../Ebaileyi.chr.genome.fa

I reworked the code, and here's what happened.

[anxuan-web]

And I will report an error when I run collapse. flair collapse -g ../GS209-2.chr.final.fasta -q flair_all_corrected.bed -r ../../01.nanofilt/filt.GS_02_lung.fq.gz -o out/collapse --gtf ../GS.filter.final.gtf --stringent --check_splice --generate_map --annotation_reliant generate

[Jeltje]

It looks like your GY_01_lung.bed contains chromosomes not present in your GY.new.all.genome.gtf Here's how to find what's missing: cut -f1 GY.new.all.genome.gtf | sort -u > genome.chrs cut -f1 GY_01_lung.bed | sort -u > lung.chrs comm -3 genome.chrs lung.chrs # first column gives anything unique to genome, second is for lung

You might also want to make sure your genome file uses the same identifiers.