Hello Assaf,
The SIB Alt-splicing track has special logic for its display. Unfortunately
this logic isn't included in the Custom Track tool; it's not possible to
display
a custom track in the same way the Alt-splicing track is displayed.
You can read about the details behind a track (description, methods,
display,
credits, references) by pressing on the 'mini-button' to the left of the actual
track display, or by clicking on the hyper-linked track name in the track
controls (below the display). The description page for the Alt-splicing track
explains the steps followed to create this track:
The splicing graphs were generated using a multi-step pipeline:
1. RefSeq and GenBank RNAs and ESTs are aligned to the genome with SIBsim4,
keeping only the best alignments for each RNA.
2. Alignments are broken up at non-intronic gaps, with small isolated
fragments thrown out.
3. A splicing graph is created for each set of overlapping alignments. This
graph has an edge for each exon or intron, and a vertex for each splice site,
start, and end. Each RNA that contributes to an edge is kept as evidence for
that edge.
4. Graphs consisting solely of unspliced ESTs are discarded.
If you would like to display Alt-splicing type tracks, you could set up your
own mirror site of the Genome Browser and load it as a native track. The
Genome
Browser and Blat software are free for academic, nonprofit, and personal use. A
license is required for commercial use.
How to download the software: http://genome.cse.ucsc.edu/FAQ/FAQlicense#license3
You can obtain the source tree either via CVS:
http://genome.ucsc.edu/admin/cvs.html
or a zip file:
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
Please note the build instructions:
http://genome.ucsc.edu/admin/jk-install.html
All of the kent utilities output their usage message and command
line options by running them with no arguments.
I hope this information is helpful to you. Please don't hesitate to contact
the mail list again if you require further assistance.
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Assaf Ben-Zaken wrote:
> Dear Sirs,
> I'm interested in creating my own custom track similar to that of SIB
> Alt-Splicing in the hg18.
> I downloaded the table and figured the schema.
> However I can't upload it as a custom track.
> Is it possible to upload such a track?
> if so, which file format is it?
> How do I create altGraphX track?
> Thanks,
> Assaf
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
