I am using bedtools getfasta to convert genomic coordinates to sequences. I feed it a bedfile containing say chr1 s.start s.end. When I check the sequence output, it does not include the s.start base.
For example if the bedfile entry is chr1 23456 23678, it gets the sequence from 23457-23678. Is this a feature and I should use a tag to make it include the first base?
The command I am using is bedtools getfasta -fi genome.fa -fo gene.fa -bed input.bed
I tried this in bedtools versions 2.27.1 and 2.30.1
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BED files are 0-based. I link this old but gold biostars thread for more background. Essentially, from normal counting with start 1 you subtract 1 from the start coordinate.
For example in the sequence ATCGGG the TCGGG substring would have "normal" (aka human-readable) coordinates 2-6, but in BED format that would be:
chrSomething 1 6
Here is the bedtools "proof":
$ cat foo.bed
chrSomething 1 6
$ cat foo.fa
>chrSomething
ATCGGG
$ bedtools getfasta -fi foo.fa -bed foo.bed
>chrSomething:1-6
TCGGG
