Hello Mark,
Not all genomes in the database assignment list are pre-index for all
tools. That is the case for this genome. We can consider add this in,
but it would actually be quicker for you to simply load a fasta version
of the genome into your history and use it as a custom reference genome
from there.
Most tools have some variation of the choice on the SAM->BAM tool form's
option: "Choose the source for the reference list:" set as "History".
Load the genome using FTP, as explained here:
http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP
Best wishes for your project,
Jen
Galaxy team
On 10/24/11 7:46 AM, Mark Silby wrote:
Hi all,
We are just beginning to analyze RNA-seq data and hope to make use of
the Galaxy tools. We are not using a commonly studied organism such as
human. Rather, our data are from the bacterium Pseudomonas fluorescens
Pf0-1.
The genome for P. fluorescens Pf0-1 appears in the "database/build"
menu, and we have selected this in the .sam file attributes.
When we run the sam to bam conversion, we get the error "Sequences are
not currently available for the specified build."
Is this something that can be corrected easily?
Many thanks for your help.
Mark Silby
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Jennifer Jackson
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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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