How to fetch genomic coordinates from fasta?

Question

[bioinforupesh2009.au]

Hello all,

I would like to have genomic positions (BED/GFF/GTF) of my multifasta sequences from genome. I know that if I have any bed/gff (genomic positions) then I can extract seq (in fasta) by bedtools but here my case is opposite.

Any idea?

Thanks

Answer 1

[Sukhi Singh]

You have to map first as Juan said, for short reads you'll get sam/bam and then you can use bamToBed

Answer 2

[JC]

Just align your sequences to the genome (Blast or Blat for long sequences, Bowtie, BWA, STAR for short sequences) and extract the coordinates.