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Bedtools Merge .bed file with unique ID column

Hello,

I have added a unique ID column (as shown below) to my .bed file so I can identify merged elements after merging has occurred.

chr4    132181662   132181672   HG00365_1k
chr4    132181662   132181672   HG00368_1k
chr4    132181662   132181672   HG00369_1k
chr4    132181662   132181672   HG00371_1k

After merging I receive:

chrX    68861391        68861401        2
chrX    70102169        70102179        2
chrX    71312620        71312630        125
chrX    72343223        72343233        16

Is there a specific code that allows me to see which IDs have been merged?

Thank you in advance.

bed bedtools
• 2,308 views • link
updated by Ram Ram • written by reece • reece

1 answer

Figured it out this seems to have worked:

bedtools merge -i test.bed -d 500 -c 4 -o collapse
• 0 views • link
updated by ATpoint ATpoint • written by reece • reece

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