Hi All, Can some one tell me the parameters used in the Galaxy "Mapping Illumina with Bowtie" defined as the "common settings"? I was trying to replicate the results from Galaxy using my own desktop installation of Bowtie but they differ by a rather big margin. Thanks much, Yongde On Mon, Apr 29, 2013 at 1:06 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hello Yongde,
The list of genomes is gathered from many sources and is comprehensive to facilitate external display functionality (at UCSC - main and microbial-, Ensembl, Wormbase, etc.). When assigning a dataset in a standard format to one of these sources, those available will appear as links within the dataset's box.
Trackster (Galaxy's native visualization tool) is available to most common data formats, even in the absence of an assigned database, through the use of the Custom Reference Genome function (aka "Custom Build"). We think this is a great advantage, in particular for cases such as yours - since you don't have restrict yourself to external applications that happen to host your genome. Click on the link here and select "Trackster" to give it a test run:
The Custom Reference Genome function is also intended to be used for smaller genomes such as this one when performing alignments and most other jobs - no pre-indexing of the genome is necessary. Simply load the genome in fasta format as a dataset and use it with tools, using a "reference genome from the history". The rational is that these are many, small, easily indexed during the course of job processing, and provides immediate access to genomes that are either newly published, or not widely used, or simply too numerous as a whole class for us to practically process in full and keep current.
We have detailed help about how to use the Custom Reference Genome method, including troubleshooting help should you need it, although in practice you will likely find this to be fairly simple with 2-3 preparatory steps, depending on the source. Most if not all of these can be done within Galaxy. http://wiki.galaxyproject.org/Support#Custom_reference_genome
Hopefully this helps. If you do need more guidance, please let us know,
Best,
Jen Galaxy team
On 4/29/13 9:01 AM, YBao wrote:
Hi All,
I was trying to map a set of data to a genome, Klebsiella pneumoniae subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able to find the reference genome as listed above. However, when I tried to map the data using wither bowtie or BWA, the pull down list did not include this genome. Can someone help or enlighten me as why it did not make into the list?
Thanks
Yongde
-- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA
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-- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA
