Hi again,
A small correction that simplifies the process. Please see below.
On 8/6/10 6:24 PM, Jennifer Jackson wrote:
Hello Antony,
Yes, to do this, create your own reference index, load it into your history (ftp/http load), and specify that index for mapping.
NGS: Mapping -> Map with Bowtie for Illumina
Will you select a reference genome from your history or use a built-in index?: "use one from the history"
At this step, select the reference sequence fasta file from your history and set indexing parameters (all on the same form). No need to pre-index!
So, skip all the this:
You will need the Bowtie distribution to do the indexing. Here is a link to the tutorial help for the process and the source (if you don't have it already). http://bowtie-bio.sourceforge.net/tutorial.shtml#newi http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.5
Best,
Jen Galaxy Team
On 8/6/10 12:42 PM, Antony Jose wrote:
Hi, I am a relatively new user to Galaxy. Of the 21 million mappable illumina reads, 17 million mapped to a reference genome. I would like to know if the remaining 4 million come from a known contaminating sequence for which I have a .txt file. Is there an easy way of doing this in Galaxy? Please advice. Thank you. Antony _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user