Displaying Bed file in IGV

Question

[cpn239]

Hi,

I am trying to upload Bed files into the IGV but I am having trouble seeing anything. The Bed file looks like this in text editor:

chr6    124750660    124750661    45    0.444444444444444    *    124750660    124750661    0,28,0
chr6    124752481    124752482    60    0.133333333333333    *    124752481    124752482    0,187,0
chr6    124752491    124752492    77    0.025974025974026    *    124752491    124752492    0,242,0

Should this format be okay?

Thanks!

[Devon Ryan]

Your example works for me. Just zoom in a bit more if nothing shows up at first.

[Istvan Albert]

make sure that you have tabs and not spaces between columns

Answer 1

[andrew.j.skelton73]

Try running it through IGV tools to convert the format and see if it throws an error? How big is the bed file, it may be that it's simply loading into memory. If you don't give the java heap enough memory initially, it'll continually be requesting more memory as it loads in the file, as such, that can be quite slow.