Can Galaxy help with Comparative Genomics?
The lab I work with would like to compare a few populations' genomes of a species with an unpublished genome assembly.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
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The lab I work with would like to compare a few populations' genomes of a species with an unpublished genome assembly.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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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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
participants (3)
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Jennifer Jackson -
Joshua Burkhart -
Joshua Burkhart [uoregon.edu]