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Question: Mapping Unmapped Sequences To Other Guessed Contaminants
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gravatar for Antony Jose
8.3 years ago by
Antony Jose • 70
Antony Jose • 70 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 • 1.1k views
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modified 8.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 8.3 years ago by Antony Jose • 70
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gravatar for Jennifer Hillman Jackson
8.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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" 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 -- Jennifer Jackson http://usegalaxy.org
ADD COMMENT • link written 8.3 years ago by Jennifer Hillman Jackson ♦ 25k
Hi again, A small correction that simplifies the process. Please see below. 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: -- Jennifer Jackson http://usegalaxy.org
ADD REPLY • link written 8.3 years ago by Jennifer Hillman Jackson ♦ 25k
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