How to fetch genomic coordinates from fasta?

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

r rna-seq gene sequence

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updated 3.4 years ago by Ram

• written 12.2 years ago by bioinforupesh2009.au •

2 answers

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

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written 12.2 years ago by Sukhi Singh

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

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written 12.2 years ago by JC

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