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subseq return fasta with feature name from GFF #89
Description
Hi Wei,
I wonder whether the seqkit subseq can return fasta files with the feature name in the fasta name.
For example, run seqkit subseq --gtf Osativa_323_v7.0.gene.gff3.gz --chr Chr5 --feature gene Osativa_323_v7.0.fa.gz>test.fa will return fasta files with the gene name in the fasta name. Something like >GENENAME_LOCATION
Currently, it returned the location as the fasta name.
>Chr5_4003-4356:+
Anyhow, very nice tool!
Best,
Ji
Activity
shenwei356 commentedon Nov 2, 2019
gff file is not supported, you may need to convert feature files.
timedreamer commentedon Nov 2, 2019
Thank you for the quick response. I will try to convert gff3 to gtf after I'm back to work.
timedreamer commentedon Nov 2, 2019
Solved. You are right. It works after converting gff3 to gtf and doing some modifications on the gtf file.
Thanks!