Hello Galaxy Team,
I am writing to request that the genome of *Sinorhizobium meliloti
added to the "Map with Bowtie for Illumina" tool. I am using the main
server http://main.g2.bx.psu.edu/ and my user name is mbiggs.
Please let me know if this email is received.
The quickest way to use new genomes with most tools, including Bowtie,
is to use them as a custom reference genome. To do this, load the
in fasta format into your history.
Then, on the tool form (for Bowtie, will vary slightly between tools),
Will you select a reference genome from your history or use a
built-in index?: "Use one from the history"
The form will refresh, them set:
Select the reference genome: "dataset_for_your_loaded_genome"
1 - double check that the format is strict fasta (all lines wrapped
to same length, no extra lines or hidden characters, sequence entries
are unique within file).
2 - use the same genome dataset for all steps within an analysis
3 - load using FTP and make certain load is complete
Hopefully this helps!
I am not sure what you mean by an annotated genome, would you be able
send more details?
Meanwhile, I can let you know that the tools that use a reference
(custom or native) all expect a fasta formatted input and use the data
directly or create indexes from the data. Any DNA (and sometime RNA)
nucleotide fasta file can be used and whether using something other
a complete genome makes sense scientifically is up to the user to