Question: How Best To Add Custom Variation Track To Ucsc Browser?
7
gravatar for Ian
8.6 years ago by
Ian5.4k
University of Manchester, UK
Ian5.4k wrote:

I have generated sequence variants (SNPs/INDELs) by NGS resequencing and would like to display them on the UCSC browser (I have resequenced against a UCSC reference genome). Obviously i could use BED files for SNPs, but does anyone know the best way to upload SNPs/INDELS in a custom track?

indel variant snp ucsc • 3.1k views
ADD COMMENTlink written 8.6 years ago by Ian5.4k
4
gravatar for Alastair Kerr
8.6 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

I use an in-house galaxy server for all my coordinate data. It provides links to display your data uploaded into your history on both UCSC and ensembl automatically - assuming you have filled in the metadata for the species build for the correct species.

ADD COMMENTlink written 8.6 years ago by Alastair Kerr5.2k
1

It isn't that i don't know how to display my own data in UCSC, but what is the best way to present SNP, insertion and deletions relative to the reference sequence. SNPs are simple as they are just simple coordinates, but INDELS are a bit more of a challenge. Thanks anyway.

ADD REPLYlink written 8.6 years ago by Ian5.4k
1

Why not use an use an interval or wiggle file: chromosome, start, stop and value, where value = the size of the indel, negative for deletion, positive for insertion

ADD REPLYlink written 8.6 years ago by Alastair Kerr5.2k

Interesting! The samtools pileup format does anchor insertions and deletions to coordinates of the reference genome. If there isn't an existing method, then i will certainly pursue this.

ADD REPLYlink written 8.6 years ago by Ian5.4k
2
gravatar for brentp
7.6 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

I wrote up one method of doing this here: https://gist.github.com/1232981

UCSC recently added the ability to render VCF as a custom track.

ADD COMMENTlink written 7.6 years ago by brentp23k

Smashing! Thanks for picking up on this old thread.

ADD REPLYlink written 7.6 years ago by Ian5.4k
1
gravatar for Ian
8.6 years ago by
Ian5.4k
University of Manchester, UK
Ian5.4k wrote:

The helpful people from UCSC browser sent me a link http://genome-test.cse.ucsc.edu/FAQ/FAQformat.html the bottom of which describes the 'Personal Genome SNP format' which can be used as a custom track. But this does not appear to handle INDELS. This is currently only for the TEST browser.

ADD COMMENTlink written 8.6 years ago by Ian5.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1177 users visited in the last hour