Question: mapping over lapping genes to CNV probes
0
gravatar for george.wiggins
3.1 years ago by
New Zealand
george.wiggins0 wrote:

I am very new to galaxy. I have CNV call data which has a start position and stop position for the genomic region of variation. What I want to do is pull out the genes that over lap these probe position, but unclear on how to do this. 

galaxy • 523 views
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson24k • written 3.1 years ago by george.wiggins0
0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

The tools in the groups "Operate on Genomic Intervals" and  "NGS: BED Tools" will intersect two datasets of genome coordinates. Obtain the reference annotation for genes/transcripts from UCSC, Ensembl, Biomart, etc. 

It is important that the reference genome associated with your calls and with the reference annotation are an exact match, and that both exactly match the reference genome used in Galaxy. Here is how to check:
http://wiki.galaxyproject.org/Support#Reference_genomes

Best,
Jen
Galaxy team

 

ADD COMMENTlink written 3.1 years ago by Jennifer Hillman Jackson24k
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