Intersecting regions in the genome

Question

[pixie@bioinfo]

I had written a python code which outputs list of lists of start and end positions of chromosomal coordinates corresponding to certain GC% bins

for example,

GC_10: [[20451, 20500], [32451, 32500], [38301, 38350]] GC_50: [[615051, 615100], [616501, 616550], [622201, 622250], [623301, 623350]]

I have generated these for all chromosomes

I have another list of chromosome regions, as we get from normal blast hits, chr1: 685701..702450

I want to find out to which all bins my blast hits lie approximately. Any help ?

Answer 1

[ATpoint]

You should save these coordinates in BED format and then use bedtools, either intersect or closest depending on the exact aim.

[pixie@bioinfo]

Okay, Thanks I am looking into this