Generating a Bed file from a Fasta file

Question

[pirku]

I created many random sequences by using NullSeq 2.0, and saved those sequences in a fasta format. Now I want to get the genomic coordinates and make a bedfile. Any ideas on how to do that?

[Pierre Lindenbaum]

you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.

[pirku]

I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned

match   mis-    rep.    N's Q gap   Q gap   T gap   T gap   strand  Q           Q       Q       Q   T           T       T       T   block   blockSizes  qStarts  tStarts
        match   match       count   bases   count   bases           name        size    start   end name        size    start   end count
---------------------------------------------------------------------------------------------------------------------------------------------------------------

[Pierre Lindenbaum]

there is not enough information. you have to show us the command you used, a snapshot of your fasta...