So I have recently joined a new lab and my first project is to locate and generate heat maps of exon-intron junctions. I am using the UCSC Genome Browser to find a exon start site for all annotate genes.
Needless to say I'm pretty lost. Was hoping someone could guide me through the process.
Thank you in advance!
1 answer
Go to the UCSC table browser, then select the relevant genome/assembly/group/track based on your model organism, set your output format to BED and click get output, the next window should allow you to create a single BED record per coding exon
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James Ashmore
Sure, just use something like bedtools closest to annotate your peaks with the closest or overlapping coding exon.
A file with a .bdg extension is usually in bedGraph file format, check the UCSC definition of the bedGraph format for help.
Managed to do everything just fine. But while trying to view my heatmaps in Java ViewTree I come upon this error and can't seem to find anything on it.
error parsing File: LoadException 1: Error Parsing CDT: java.lang.ArrayIndexOutOfBoundsException: 203
parse cannot succeed. please fix.
I realize you might not be familiar with the software, but any ideas?
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