Question: Display Bed In Igv
1
gravatar for camelbbs
6.8 years ago by
camelbbs660
China
camelbbs660 wrote:

Hi all,

Happy new year.

Here I want to ask a question about how to show bed files in IGV.

My bed file is like this:

chr1    34611   35174   uc001aak.1  2.2      -
chr1    35277   35481   uc001aak.2  1.5       -
chr1    35721   36081   uc001aak.3  0.5       -
chr1    69091   70008   uc001aal.1  0.9       +

The 5th column is the pileup.

Anybody know how to display this kind of bed file in IGV to show the pileup level? Thanks a lot.

igv • 3.0k views
ADD COMMENTlink modified 5.7 years ago by Biostar ♦♦ 20 • written 6.8 years ago by camelbbs660
2
gravatar for sah9b
6.8 years ago by
sah9b100
United States
sah9b100 wrote:

You probably want to turn it into a bedGraph file. That is, remove the UCSC IDs and strand information so your file has 4 fields: chr, start, end, and pileup level.

ADD COMMENTlink written 6.8 years ago by sah9b100

Thanks a lot!...

ADD REPLYlink written 6.8 years ago by camelbbs660
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