Export fasta from TALON database?

[joelnitta]

Hi, thanks for the excellent software!

This is a feature request, or if there is a way to do this already, I'd like to know how. I want to export a "transcriptome" of all filtered isoforms for downstream analysis. This is basically the same thing as talon_create_GTF, but instead of a GTF file it would produce a fasta file. I tried using gffread to extract the transcript sequences from the GTF + genome, but this results in the sequences in the genome where the isoforms mapped to, not the isoforms themselves.

Thanks!

[fairliereese]

This is an interesting idea. I am a bit confused though, wouldn't the sequences in the genome where the isoforms mapped to be the transcript sequences themselves? Unless you're concerned with pulling out genetic variation as compared to the reference genome.