I am trying to run Extract Genomic DNA on a bed file in which I have an ID, the start coordinate and the end coordinate. The sequences I am targeting represent products for potential primers (~180 of them total).
The Coordinate file set up:
Chrom Start End
chr1000 184143 184871
The file I am matching it to is a set of ORFs that I extracted from a Blast search in the following format:
I have both files assigned to my custom build for the organism. When I try to run this, however, I get the error:
181 warnings, 1st is: Unable to fetch the sequence from ‘184143’ to ‘171’ for chrom 'chr1000 '.
Skipped 181 invalid lines, 1st is #1, “chr1000 184143 184314”
I think I have made the formats of the chromosome names as identical as they get, but why will this still not function? I was wondering if it came to a matter of tabs vs spaces?
Any ideas are helpful.Thanks!
EDIT: I tried converting my bed file to tab delimited (just in case even though I saved it as tab-delimited) and tried again, and it still is saying all my lines are invalid.