Question: Re: [Galaxy-Bugs] Cdna Mapping 454
7.8 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
Hi Chris, I'm cc'ing galaxy-user because your questions are more about use than bugs. You're correct here. I looked through the LastZ documentation but didn't see anything that would support mapping cDNA to a reference genome. You could try this, but splicing is likely to prevent good mapping. A better alternative is to use Tophat: http://tophat.cbcb.umd.edu/ Tophat is a splice junction mapper; Tophat, among other outputs, provides a list of mapped reads in SAM format. We have a very simple version of Tophat running on our test server that you try out: http://test.g2.bx.psu.edu/ We'll have a more complete version of Tophat up in the next day or two. A caveat: Tophat is designed for Illumina data, so you may not get optimal results when using 454 data. Best, J.
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