ALTgraphX splice map

[Shreeharsha Thipperudrappa Tarikere, Dr]

Hi 

I am a staff scientist at McGill. I am trying to display my RNAseq alignment bam, and bed files as an ALTgraphX splice map in UCSC custom track. What do I need to do show such an alternative splice map as a custom track.

Thanks 

Best

Hasrah

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

The following help page will guide you through uploading a BED and a BAM custom track.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks

A custom track is defined by three lines: the browser line, the track line, and the data lines. The browser
and track lines control the configuration options when you load the custom track. The data lines are the
annotations that you are displaying on the UCSC Genome Browser. A BED custom track is text-based and
can be uploaded directly to the UCSC Genome Browser. A BAM file is binary indexed and will require you
to host the BAM file on a remote server that accepts byte-range requests. The "bigDataUrl" parameter in
the track line specifies where the UCSC Genome Browser should fetch the data. Here are examples of
browser lines, track lines, and data lines for a BED and BAM custom tracks:

browser position chr21:33031596-33041570
track db='hg19' name='1 bed3' priority='10' description='CT testing type = bed 3' visibility=pack
chr21    33031596    33034920
chr21    33034920    33038244
chr21    33038244    33041570
track type=bam priority='140' name='19 BAM Example One' description='Bam Ex. 1: 1000 Genomes read alignments (individual NA12878)' pairEndsByName=. pairSearchRange=10000 chromosomes=chr21 bamColorMode=gray maxWindowToDraw=200000 db=hg19 visibility=pack bigDataUrl=http://genome-test.gi.ucsc.edu/goldenPath/help/examples/bamExample.bam

To view the BAM file, you may be interested in using a new feature we are providing, Hub Space.
With Hub Space, users get 10 GB of storage for free, which can be expanded if needed. If you have
the BAM file on your local computer, you can upload the file to Hub Space, and the feature will
automatically create a track hub for you.

https://genome.ucsc.edu/cgi-bin/hgHubConnect?#hubUpload

As this is a new feature, any feedback or suggestions you have are happily appreciated.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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