Cooler digest with 2 restriction enzymes

[ddepierre]

Hi cooler people,

Is it possible to use cooler digest with 2 restriction enzymes?

Something like:
cooler digest --rel-ids 0 --out mm10_DpnII_DdeI_restriction_sites_cooler_digest.bed chrNameLength.txt mm10.chroms.all.fa DdeI, DpnII

or an alternative with cooltools genome digest like:
cooltools genome digest chrNameLength.txt mm10.chroms.all.fa DdeI,DpnII

Thanks for support,
David

[ddepierre]

Alternatively, can you confirm I can do it with

mm10_DdeI_restriction_sites_cooler_digest_3cols.bed = rtracklayer::import.bed('mm10_DdeI_restriction_sites_cooler_digest_3cols.bed')
mm10_MboI_restriction_sites_cooler_digest_3cols.bed = rtracklayer::import.bed('mm10_MboI_restriction_sites_cooler_digest_3cols.bed')
mm10_DdeI_MboI_restriction_sites_cooler_digest_3cols.bed = GenomicRanges::disjoin(c(mm10_DdeI_restriction_sites_cooler_digest_3cols.bed, mm10_MboI_restriction_sites_cooler_digest_3cols.bed))
rtracklayer::export.bed(mm10_DdeI_MboI_restriction_sites_cooler_digest_3cols.bed, 'mm10_DdeI_MboI_restriction_sites_cooler_digest_3cols.bed')

Giving this, combining the blue and the green in the red one:

Best,
David

[nvictus]

cooler digest does not support multiple enzymes, though this is something we can add, since it uses biopython under the hood which can do this. EDIT: on closer inspection, I'm not sure it can.

Alternatively, can you confirm I can do it with

If I understand correctly what GRanges disjoin is doing (cutting out overlapping ranges as separate intervals), then, yes, this makes sense!