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Published 20 hours ago • verified publisher icon tseemann

GFF?

Open lskatz opened this issue 2 years ago • 4 comments

Does anyone have a nice one liner to get GFF out of abricate output?

lskatz avatar Jul 01 '22 18:07 lskatz

n/m I guess BED will do it for me

cut -f 2-4 *.abricate.tsv | tail -n +2 > abricate.bed

lskatz avatar Jul 01 '22 18:07 lskatz

lskatz Thank you for asking the question and providing the partial solution (excuse me as I could not write a proper gff3 after your steps). Could you please elaborate if you found a solution to this? Any solution https://github.com/tseemann (even if multi-step solution)?

com31 avatar Mar 20 '23 17:03 com31

My solution gives a bed file, and then if that is not sufficient, you can convert to a GFF from there. People have some partial solutions for that but I guess there isn't an exact conversion to GFF from BED.

For example: https://bioinformatics.stackexchange.com/questions/2242/how-to-convert-bed-to-gff3

lskatz avatar Mar 20 '23 18:03 lskatz

Thank you lskatz for your help. A discussion and developing solution is here [https://bioinformatics.stackexchange.com/questions/20749/convert-abricate-output-tsv-file-to-gff3-format] Could you too please help?

com31 avatar Mar 22 '23 14:03 com31