Hi Scott,

If your Illumina data is DNA, then using either Bowtie (no indels) or BWA (supports indels) with the known sequence as a 'custom reference genome' would be a good choice.


If RNA, then doing the same, but using TopHat instead, would be recommended.

To use your known sequences as a custom reference genome, first load it in fasta format as a dataset into your history. Then at run time set the mapping tool form options to use a reference genome 'from the history'. There's no criteria around the actual content of a reference genome (can be a single short sequence), but the format should be standard fasta.
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome

Please let us know if you need more assistance,

Best,

Jen
Galaxy team

On 4/18/12 4:15 AM, Scott Tighe wrote:
Galaxy

What is the best method in Galaxy to compare a Illumina data set to a
1500 bp known sequence?

Scott

Scott Tighe
Advanced Genome Technology Lab
Vermont Cancer Center at the University of Vermont
149 Beaumont Avenue
Health Science Research Bd RM 305
Burlington Vermont USA 05405
lab 802-656-AGTC (2482)
cell 802-999-6666


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