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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http://usegalaxy.org
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
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