Bedtools intersect 0- and 1-based coordinate files
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5 months ago

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!

gff intersect bedtools bam • 290 views
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Entering edit mode
5 months ago
ATpoint 55k

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    .   +
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Ah wonderful, good to know! Brilliant answer and thanks for the code / outputs to back it up.

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