This page has a simple breakdown of how to call variants within Galaxy.
This is brand new, so full annotation/video is pending, but it should
still be straightforward to see how the data is prepped and which tools
Another set of tutorial videos cover the tools, which you can use on the
public site or on a scaled up cloud server as needed:
Hopefully this help you to get started.
On 10/21/12 3:11 PM, Xiefan Fang wrote:
Dear galaxy users,
We have done deep sequencing on some known genomic loci using
Hiseq2000. I have already mapped the reads to the reference sequences
by using Galaxy. In the next step, I want to find SNPs and calculate
the SNP percentage within the reads. There are 500,000 to 1,000,000
reads per biological sample. Can I do it with galaxy? If not, is there
other programs available in windows? Considering that I am not very
familiar with programming.
University of Florida
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