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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