isoform file not available

[Kiliankleemann]

I don´t have an isoform.txt file, can I still convert bed to gtf?

[alejandrogzi]

Hi @Kiliankleemann,

Not at this time. bed2gtf was build with the goal to make the conversion faster but complete (including gene_ids); however, I can consider to make it an option (maybe a flag --no-gene (?)) in the next release.

If you need that functionality right now, I think the best option is to use UCSC's C binaries (bedToGenePred + genePredToGtf)

Best,
Alejandro

[alejandrogzi]

Hey @Kiliankleemann

Just to let you know that now you can convert any bed into gtf without a isoforms.txt by simply specifying --no-gene, something like this:

bed2gtf -b your.bed -o out.gtf --no-gene

Best,
Alejandro