Extract all BED intervals between genomic coordinates

Question

[michael.ridley6]

Trying to extract some DNAse HS peaks (I have the peaks as BED file), which tool would be best to use to extract all the peaks, between a set of genomic coordinates?

[Jeffin Rockey]

Wouldn't a bedtools intersect with the peaks bed and the coordinates bed suffice?

[Medhat]

yes indeed :)

bedtools intersect [OPTIONS] -a <FILE>  -b <FILE1, FILE2, ..., FILEN>

http://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

[Medhat]

Did you had a look at plink

[Devon Ryan]

In addition to the other options, you can also tabix index the file and then use tabix.

Answer 1

[Alex Reynolds]

You can use BEDOPS bedops --element-of 1 to get peaks that overlap regions of interest by one or more bases:

$ bedops -e 1 peaks.bed regions.bed > answer.bed

If you want peaks that are completely contained inside regions, replace 1 with 100%:

$ bedops -e 100% peaks.bed regions.bed > answer.bed