How to assign Active Enhancer to every genes within 10 kb region?

chr1 34737 34937 7_Weak_Enhancer 0 . 34737 34937 255,252,4 chr1 35737 35937 7_Weak_Enhancer 0 . 35737 35937 255,252,4 chr1 36137 36337 7_Weak_Enhancer 0 . 36137 36337 255,252,4

chr1 34737 34937 7_Weak_Enhancer 0 . 34737 34937 255,252,4|chr1 24610 44610 NR_026820 FAM138F - chr1 35737 35937 7_Weak_Enhancer 0 . 35737 35937 255,252,4|chr1 24610 44610 NR_026820 FAM138F - chr1 36137 36337 7_Weak_Enhancer 0 . 36137 36337 255,252,4|chr1 24610 44610 NR_026820 FAM138F -

chr1 34737 34937 7_Weak_Enhancer 0 . 34737 34937 255,252,4|chr1 24610 44610 NR_026820 FAM138F - chr1 34737 34937 7_Weak_Enhancer 0 . 34737 34937 255,252,4|chr1 24610 44610 NR_026820 FAM138F - chr1 34737 34937 7_Weak_Enhancer 0 . 34737 34937 255,252,4|chr1 24610 44610 NR_026820 FAM138F -

3.5 years ago by

Alex Reynolds ♦ 30k

Seattle, WA USA

Alex Reynolds ♦ 30k wrote:

You would use bedmap instead of closest-features to map (or associate) all genes to enhancers. Add the --range N operand to pull in associations over N bases around the reference elements (enhancers), say a 20 kb window:

$ bedmap --range 10000 --echo --echo-map enhancers.bed genes.bed > answer.bed

The --echo-map operand gives you all the detail about mapped genes. There are other --echo-map-* operations to get a subset of data about mapped genes; see --help or the documentation for more information.

ADD COMMENT • link modified 3.5 years ago • written 3.5 years ago by Alex Reynolds ♦ 30k

Thanks a lot Alex for replying. I have a little problem, I already tried this way as you suggested in your answer in old question but the problem is I get all the overlaps in one line separated by ;. While I want the answer in the format as mentioned above in the question. Currently what I'm getting for my sample input file is: chr1 500 1000 Enh1 3.45 5.67|chr1 1500 2500 NR_9088 ATF2 -;chr1 11000 12000 NR_879 ATF1 +;chr1 19000 21000 NR_876 ATF1 + while what I want is:

chr1    500 1000    Enh1    3.45    5.67|chr1   1500    2500    NR_9088 ATF2    -

chr1    500 1000    Enh1    3.45    5.67|chr1   11000   12000   NR_879  ATF1    +

chr1    500 1000    Enh1    3.45    5.67|chr1   19000   21000   NR_876  ATF1    +

ADD REPLY • link written 3.5 years ago by Bioinformatist Newbie • 250

You can pipe to awk to reformat the output, e.g.:

$ bedmap --range 10000 --echo --echo-map enhancers.bed genes.bed | awk -F'|' '{ reference = $1; mappings = $2; n = split(mappings, m, ";"); for(i = 1; i <= n; i++) { print reference"|"m[i]; } }' > answer.bed

This could blow up the file, if you have a lot of overlaps. I suggest using standard input and output streams where you can, to minimize file sizes or the writing of intermediate files.

ADD REPLY • link modified 3.5 years ago • written 3.5 years ago by Alex Reynolds ♦ 30k

Yes, it works. A little problem left is: I'm trying to use --delim '\t' after the --echo-map but it is not working. can you guide me if I'm doing something wrong here? This is what I am trying: bedmap --range 20000 --echo --echo-map --delim '\t' enhancers.bed genes.bed | awk -F'|' '{ reference = $1; mappings = $2; n = split(mappings, m, ";"); for(i = 1; i <= n; i++) { print reference"|"m[i]; } }'

ADD REPLY • link written 3.5 years ago by Bioinformatist Newbie • 250

I can do it by using sed -i 's/|/\t/g' answer.bed but I was wondering why the --delim "\t" is not working !!

ADD REPLY • link written 3.5 years ago by Bioinformatist Newbie • 250

If you switch the --delim character from the default pipe character (|) to a tab character (\t) then you will no longer be able to use | in awk as a field separator between the reference element (reported by --echo) and the mapped elements (reported by --echo-map).

You could use sed at the very end, but you probably want to keep that | character around until then, so that you have a delimiter between reference and mapped elements that is something other than a tab character. This is because the delimiter between fields inside a reference element and inside one or more mapped elements is also a tab character, and so that makes separation more difficult.

ADD REPLY • link modified 3.5 years ago • written 3.5 years ago by Alex Reynolds ♦ 30k

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