Mapping Unmapped sequences to other guessed contaminants
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
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" 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
-- Jennifer Jackson http://usegalaxy.org
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
-- Jennifer Jackson http://usegalaxy.org
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