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Question: Observing merged genomic intervals along with their original unmerged intervals
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gravatar for arsala521
12 months ago by
arsala521 • 10
arsala521 • 10 wrote:

Hello everyone,

Is there any option in bedtools or bedops that after merging show the original regions of the merged interval as well?

For example for the following input

chr1 500 1000
chr1 750 1000
chr2 200 500

can I have the output somewhat like this

chr1 500 1000 chr1 500 1000 chr1 750 1000
chr2 200 500

For every merged region, I want to see the original regions along with it.

Thank you
merging bedtools • 199 views
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modified 11 months ago by Kevin Blighe ♦ 71k • written 12 months ago by arsala521 • 10
0
gravatar for Kevin Blighe
11 months ago by
Kevin Blighe ♦ 71k
Republic of Ireland
Kevin Blighe ♦ 71k wrote:

There is definitely an awk solution here; however, you may try out BEDTools:

cat test.bed 
chr1    500 1000
chr1    750 1000
chr2    200 500

bedtools merge -i test.bed -c 1,2,3 -o distinct -delim " "
chr1    500 1000    chr1    500 750 1000
chr2    200 500     chr2    200 500

Give that a try.

Kevin
ADD COMMENT • link modified 11 months ago • written 11 months ago by Kevin Blighe ♦ 71k
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