Expected Transcriptome BLAST

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Expected Transcriptome BLAST

Colicchio, Jack M
Hey,

Jack Colicchio here, a PhD. student at KU.  I am about to get an illumina Next gen transcriptome data setthat I would like to align and quantify against a list of expected transcripts from Mimulus guttatus.  The expected transcripts are in .gff format, and I was wondering how I could get that file uploaded to you're website to allow me to align my transcriptome against.  I successfully uploaded the .GFF file, and can view it on your site, but do not know how I could blast my .fastq data from illumine against this file.

Thanks,
Jack


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Re: Expected Transcriptome BLAST

Colicchio, Jack M
Also, I'm working under John Kelly and Lena Hileman at KU.   We, along with our collaborators at Duke, would get a lot of use out of an expected transcriptome that we could blast illumine data against.  If we sent you our genome in .fasta format along with the .gff expected transcript file is their anyway you could combine these into a database we could align against?

-Jack


On Nov 2, 2011, at 12:03 PM, Jack Colicchio wrote:

> Hey,
>
> Jack Colicchio here, a PhD. student at KU.  I am about to get an illumina Next gen transcriptome data setthat I would like to align and quantify against a list of expected transcripts from Mimulus guttatus.  The expected transcripts are in .gff format, and I was wondering how I could get that file uploaded to you're website to allow me to align my transcriptome against.  I successfully uploaded the .GFF file, and can view it on your site, but do not know how I could blast my .fastq data from illumine against this file.
>
> Thanks,
> Jack




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Re: Expected Transcriptome BLAST

Jen Hillman-Jackson
In reply to this post by Colicchio, Jack M
Hello,

To use a custom genome with the alignment tools at Galaxy Main
(http://usegalaxy.org), the dataset must be in fasta format. If the data
is RNA, then using the tools in "NGS: RNA Analysis" will accept both a
reference custom genome and a transcript file in GTF format to guide
placement (using TopHat as the preferred alignment tool).

It is important to note that the Main Galaxy site does not offer a BLAST
option (with the exception of Megablast against a specific set of
genomes), but a local or cloud instance would, using the BLAST tools in
the tool shed and setting up your own data.

Some help links:

If using the RNA Analysis tools at Galaxy Main:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP

If using a local or cloud instance:
http://getgalaxy.org
http://galaxyproject.org/wiki/Admin/Cloud
http://galaxyproject.org/wiki/Tool%20Shed

Hopefully this offers you a choice that will work for your project,

Best,

Jen
Galaxy team

On 11/2/11 10:03 AM, Colicchio, Jack M wrote:

> Hey,
>
> Jack Colicchio here, a PhD. student at KU.  I am about to get an illumina Next gen transcriptome data setthat I would like to align and quantify against a list of expected transcripts from Mimulus guttatus.  The expected transcripts are in .gff format, and I was wondering how I could get that file uploaded to you're website to allow me to align my transcriptome against.  I successfully uploaded the .GFF file, and can view it on your site, but do not know how I could blast my .fastq data from illumine against this file.
>
> Thanks,
> Jack
>
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org