Hi all,
I'm using bedtools intersect for the first time and am wondering if it performs correctly when provided with an 'A' (query) file in BAM format (which has 0-based coordinates) and a 'B' (reference) file in GFF3 format (which has 1-based coordinates).
Does bedtools intersect automatically take this difference into account? i.e. can it re-coordinate one of the files on the fly to ensure intersects are accurate to nucleotide resolution?
Cheers!
Does bedtools intersect automatically take this difference into account?
Yes, it is quite a smart one.
Example (BED vs GTF, random files I had on disk):
$ cat test.gtf
chr1 rtracklayer exon 1 2 . + . exon_id "ENSMUSE00001343744.1"; exon_rank 1; transcript_id "ENSMUST00000193812.1"; gene_id "ENSMUSG00000102693.1"; ID "ENSMUST00000193812.1"
$ cat test.bed
chr1 0 1 featureA . +
$ bedtools intersect -a test.bed -b test.gtf
chr1 0 1 featureA . +
Ah wonderful, good to know! Brilliant answer and thanks for the code / outputs to back it up.
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