chromHMM segmented genome annotation for genes
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5.0 years ago
elb ▴ 260

Hi guys, I'm analyzing chromHMM output. I opened the file _dense.bed and *_expanded.bed into IGV and I look the genes mapping into the segments of the segmented file. I would like to ask you if it is possible from the .bed file that has only 4 columns (cur, start of the segment, end of the segment, state) to assign the name of the gene mapping into the segment.

Few lines of my bed file:

 V1     V2    V3   V4
chr10   0   47100  E6
chr10 47100 48900  E4
chr10 48900 49200  E7

..............................

I just would like to add a column with the gene name in the segment

Thank you in advance

ChIP-Seq • 894 views
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