Question: How To Find Out Snps And Point Mutations In Rna-Seq Data Using Galaxy?
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gravatar for ericliaowei@gmail.com
6.5 years ago by
ericliaowei@gmail.com70 wrote:
HI, I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy server. I want find out SNP and point mutations in RNA-Seq data using Galaxy (I do not know if anyone using RNA-seq data to find point mutations, because there is whole Genome sequencing for reporting mutations and SNPs). I have been searching in the forum for a step-by-step protocols for doing it, but could not find it. I have one normal sample and two cancer samples, a TopHat produced "accepted Hits.bam" file for each one. I want to find out SNP and point mutations in the cancer samples, so How do I go from here? Can anyone show me how to do it in Galaxy main server? Thanks! Wei
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ADD COMMENTlink modified 6.5 years ago by Jeremy Goecks2.2k • written 6.5 years ago by ericliaowei@gmail.com70
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gravatar for Jeremy Goecks
6.5 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Wei, The pileup tool will help you find SNPs in your data; you'll want to read the documentation to understand how best to use it for your needs. You can also try the Unified Genotyper on our test server ( http://test.g2.bx.psu.edu/ ), but it's in alpha/beta status and we aren't providing any support for it yet. Good luck, J.
ADD COMMENTlink written 6.5 years ago by Jeremy Goecks2.2k
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gravatar for Jeremy Goecks
6.5 years ago by
Jeremy Goecks2.2k
Jeremy Goecks2.2k wrote:
Wei, The best way to move individual datasets b/t Galaxy instances is by link: right click on the dataset's save icon (a disk), copy the link, and paste that into the upload form. A couple word of caution about our test server: it is experimental and may be nonfunctional or unavailable periodically, there is little/no support is offered for new tools, and quotas are quite low. For analyses that require multiple steps, test most likely will not meet your needs. Finally, please always cc the mailing list when replying. Good luck, J.
ADD COMMENTlink written 6.5 years ago by Jeremy Goecks2.2k
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