Question

How to find list of genes nearest to list of intronic sequences

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10.0 years ago

sebastianzeki0 ▴ 240

I have a range on intronic locations in a bed file. I would like to find out the genes nearest to these sequences (and how far away they are). Is there a simple way to do this? Thanks in advance

alignment genome sequencing • 2.6k views

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by sebastianzeki0 ▴ 240

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Do you have a range to say "nearest" ? can you paste few lines of your bed file ?

ADD REPLY • link 10.0 years ago by GouthamAtla 12k

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bed file. Not sure about the range but lets say 2Mb

chr1 236079115 236079265
chr1 239828970 239829120
chr1 242340679 242340829
chr1 243847609 243847759
chr1 244879534 244879684
chr1 245910962 245911112
chr1 246134561 246134711
chr1 246250179 246250329
chr10 513705 513855
chr10 3414205 3414355
chr10 4037509 4037659
chr10 6368208 6368358
chr10 8461949 8462099
chr10 12470171 12470321
chr10 13619381 13619531
chr10 14724702 14724852

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by sebastianzeki0 ▴ 240

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OK Ill have a look at bedtools. That looks pretty good

ADD REPLY • link 10.0 years ago by sebastianzeki0 ▴ 240

Ram · Accepted Answer · 2014-12-11

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10.0 years ago

GouthamAtla 12k

Have a look at these posts:

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by GouthamAtla 12k