This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Display Bed In Igv

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
• 6,198 views • link
updated by Biostar Biostar • written by camelbbs camelbbs

1 answer

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.

• 0 views • link
written by sah9b sah9b

Thanks a lot!...

• 0 views • link
written by camelbbs camelbbs

Log in to answer this question.

More posts like this