Files in this directory represent standardized outgroup data from various sets of target enrichment probes used for enriching UCE data from various groups organisms (e.g. see [Fair:2012a]).
At the moment, the organisms having UCE/outgroup data are limited to tetrapods. This list will soon expand to include fishes.
Probe designs, genomic positions of designed probes, fasta slices around genomic positions of designed probes, and outgroup UCE loci generated from fasta slices are avaialable for various sets of probes.
You are free to use these data in your analyses. If you use the outgroup data here, please reference [Fair:2012a] and this website. You can provide the version of the data you used or provide the hash of the commit you used in the text of your manuscript, if so desired.
All of the genomic data used to generate these files are available publicly. You should reference the source of a given genomic build in your Literature Cited. A good list to find all of these sources is available by finding a given build on the UCSC Genome Browser and looking at the build details.
| [Fair:2012a] | (1, 2) Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC (2012). Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. Systematic Biology 61: 717-726. pmid: 22232343 doi: 10.1093/sysbio/SYS004. |
Files in this directory are version controlled, so if you are looking for earlier outgroup data sets, please click the tags link above to access these earlier versions.
Minor changes to the text of these documents or additional of explanatory details will generally result in a minor version bump (e.g., v3.0 to v3.1). Major changes to the contents of the repository (due to error or addition of new probes/taxa) will result in a major version bump (e.g., v3.0 to v4.0).
Working versions of outgroup data may differ, as I prepare them. The working versions may be accessed from the working branch of the repository.
The specific genome builds used for slicing data and generating outgroup UCE loci are detailed within this file.
The STEPS used to align probes, slice fastas, and assemble contigs are available within the STEPS file.
At present, the UCE outgroup loci in outgroup-loci represent the UCE locus ± 500 bp, for a total locus length of ~ 1120 bp, on average.
At the top level of the repository are several files:
- genome-sequence-location.conf provides the genome versions used to build the standardized UCE data sets and their location on my machine (the latter bits) are not likely to be useful to anyone but me
- README.rst is the file your're current reading
- STEPS.rst is a file describing the data generation steps
- uce-2.5k-probe-set contains probe designs for the 2.5k probe set and fasta slices,lastz results, and outgroup data for these probe matches against the genomes in genome-sequence-location.conf as described below.
- uce-5k-probe-set contains probe designs for the 5k probe set and fasta slices, lastz results, and outgroup data for these probe matches against the genomes in genome-sequence-location.conf as described below.
The standardized UCE data are useful in several circumstances. Within each probe-specific folder (e.g. uce-2.5k-probe-set) there are several files:
- uce-2.5k-probes.fasta provides the probe sequences we designed to data from 2.5k UCE loci
- uce-2.5k-probes.fasta.toself.lastz contains a mapping of probes to themselves to ensure that probes are unique across the set
- uce-2.5k-probes.sqlite is a database providing summary lastz data showing the mapping of probes to the various outgroup genomes in genome-sequence-location.conf
- outgroup-lastz is a directory containing the lastz results used to build the uce-2.5k-probes.sqlite database
- outgroup-fasta is a directory containing the read sliced from the various outgroup genomes in genome-sequence-location.conf and used to build the UCE loci in outgroup-loci
- outgroup-loci is a directory containing probe.matches.sqlite database and assembled contigs representing UCE loci for the taxa included. The data within this directory is useful for incorporating outgroup data to other UCE data sets as described in the phyluce documentation