Jen,
I'd like to compare the variation between genomes and will get back to
you after reviewing the resources you suggested.
Thanks!
Joshua Burkhart
On 04/28/2013 07:51 PM, Jennifer Jackson wrote:
Hi Joshua,
Do you want to compare the entire genome or just the
transcriptome/exome/variation between the two assembled genomes? Or
maybe explore both, using the combined evidence to strengthen any
conclusions?
These publications are a good overview of the tools/methods available
in Galaxy:
https://main.g2.bx.psu.edu/u/webb/p/pipeline
https://main.g2.bx.psu.edu/u/webb/p/aye-aye
The UCSC Genome browser team also creates whole genome comparison maps
- pairwise and multiple sequence alignments. These are labeled as
"Chains/Nets" and "Conservation" tracks in their browser at
http://genome.ucsc.edu. Generating this type of track would most
likely need to occur outside of Galaxy - the UCSC team are the best
ones to explain the most current processing methods:
http://genome.ucsc.edu/contacts.html. Once created, these could be
imported and used with Galaxy's tools. These publications have
examples about how this is done with MAF data:
https://main.g2.bx.psu.edu/u/dan/p/maf
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
(protocol 5)
Hopefully this offers some useful choices,
Jen
Galaxy team
On 4/28/13 4:58 PM, Joshua Burkhart [uoregon.edu] wrote:
The lab I work with would like to compare a few populations' genomes
of a species with an unpublished genome assembly. I have sequence
data for each population that was created using only single-size
insertion sequences, yielding only short paired-end reads. I was able
to create a genome assembly for one of the populations and would like
to see how it compares to another closely related species (which has
a published genome). I used Augustus
(http://bioinf.uni-greifswald.de/augustus/) to produce a GFF
annotation for my assembly but am not sure how to best go about
comparing my assembly to the published assembly of the other species.
Can Galaxy help? Are there other tools that may be of use? I tried
using ACT (http://www.sanger.ac.uk/resources/software/act/) but it
never finished. These genomes are approximately 1Gbp. Any advice
would help.
Thanks,
Joshua Burkhart
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Jennifer Hillman-Jackson
Galaxy Support and Training
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
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local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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please use the interface at:
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