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of a species with an unpublished genome assembly.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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___________________________________________________________
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