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 <j...@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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>
> --
> Jennifer Hillman-Jackson
> Galaxy Support and Traininghttp://galaxyproject.org
>
>


-- 
Yongde Bao
DNA Sciences Core
Dept. of Microbiology, Immunology,
             and Cancer Biology
UVA

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