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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