[Genome] Showing data on different chromosomes

[Shan Yang]

Hi,

I have some next generation sequencing data (NGS) that detect chimeric fusion transcripts. Basically, a pair of reads will cover two regions that are on different chromosomes. The current genome browser only allows viewing one chromosome at a time. I am wondering if you have any tool that can show that kind of data where I can view multiple chromosomes in one screen.

Thank you very much!

Shan

[Jennifer Jackson]

Hello Shan,

One idea is to use a series of Custom tracks to provide some data visualization. How to tackle NextGen sequencing & multiple genomes is an important tool development topic for us, but for now, our recommendation is as follows:

Basic plan:
1) select which chromosome to use as your "base".
2) run the sequence(s) as a BLAT against entire genome. Note the chromosome + coordinates that are not in your base chromosome. Save the results against the base chromosome as a custom track.
3) extract sequence (get DNA, Table browser) from other non-base chromosomes. BLAT this portion of non-base genomic against the entire genomic. Save results against the base chromosome as custom track.
4) open the browser window at the base location. There should be a series of custom tracks in the top group - the query sequence(s) and all non-base chromosomes.

Options:
A) the sequences will not be "aligned" to the non-base chromosomes. Therefore, you may want to do this a few times, once for each genomic location (one than one "base").
B) instead of running a BLAT to align one chromosome to another, use the Self Chain track.
C) expand BLAT alignment to not only include the component short reads but the transcript itself (if not in a track already or if modified from the public version).
D) open tracks such as Repeat Masker, Self Chain, UCSC/RefSeq genes, Conservation, and maybe also some EST/mRNA tracks for context.
E) save the results in a Session to keep them around longer and to share with others (be sure to keep backups).

Help Links:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Sessions
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks
http://genome.ucsc.edu/cgi-bin/hgLiftOver

If a better method comes up in the next few days, we will send an update.

Thank you,
Jennifer Jackson

_______________________________________________
Genome maillist - Gen...@soe.ucsc.edu
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[Angie Hinrichs]

Hi Shan,

You might also be interested in our new tool, Genome Graphs. It is
the 7th item down on the blue link bar on the left of our home page
(genome.ucsc.edu), or you can reach it directly as

http://genome.ucsc.edu/cgi-bin/hgGenome

It displays all chromosomes in a single view. You can upload your
data using a very simple format -- click on the upload button for more
info.

Hope that helps,
Angie

[Brian Raney]

Hey Shan,

We're definitely interested in displays that capture fusion products,
but none of these have made it past the grant writing phase.
If you have specific ideas about what you'd like to see,
you can send these to directly to me and I'll make sure
that they receive due consideration.

Thanks for thinking of us!

Brian Raney