Mapping Unmapped sequences to other guessed contaminants

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Mapping Unmapped sequences to other guessed contaminants

Antony Jose
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

Reply | Threaded
Open this post in threaded view
|

Re: Mapping Unmapped sequences to other guessed contaminants

Jen Hillman-Jackson
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
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-user

--
Jennifer Jackson
http://usegalaxy.org

Jennifer Hillman-Jackson
http://galaxyproject.org
Reply | Threaded
Open this post in threaded view
|

Re: Mapping Unmapped sequences to other guessed contaminants

Jen Hillman-Jackson
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
>> [hidden email]
>> http://lists.bx.psu.edu/listinfo/galaxy-user
>

--
Jennifer Jackson
http://usegalaxy.org

Jennifer Hillman-Jackson
http://galaxyproject.org