how to plot SV(structural variants) from many assemblies of a given locus
0
2
Entering edit mode
17 months ago
natalev ▴ 20

How can I visualize structural variants from multiple assemblies of a large locus (for example ~100Mb). Which program can generate a plots similar to this or something like this? enter image description here

SV • 983 views
ADD COMMENT
1
Entering edit mode

Try genome browsers/viewers, like IGV, JBrowse or UCSC. You can upload your own data to it. UCSC genome browsers supports custom coloring with the BED format.

ADD REPLY
0
Entering edit mode

Thank you! I was hoping there would be a better way to do this in order to generate good quality figures since looks like it's a common question by now.

ADD REPLY
0
Entering edit mode

what is the legend here ? X axis ? y axis ? colors ? red lines ?....

ADD REPLY
0
Entering edit mode

Each row here is assembly of a given locus (~100Mb) in the genome from one human sample. So this is looking at variation across multiple people for a given locus. Different colors represent different structural variants - inversions, duplications , deletions, etc.

ADD REPLY
1
Entering edit mode

use circos , ucsc custom tracks ....

ADD REPLY
0
Entering edit mode

Thanks a lot, for your answer!. Circos might not allow simple comparison like in the above figure showing clear structural variation (large deletions ,etc). I will try using UCSC or other viewers to see if I can compress large locus to a figure like above and clearly mark structural variants.

ADD REPLY

Login before adding your answer.

Traffic: 1796 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6