Question: Re: [Galaxy-Bugs] Cdna Mapping 454
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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.