Test dataset

This test simulation is intended to help in the development and testing of evaluation metrics. After running the short sequences through the aligner of your choice you can more quickly iterate your evaluation than on the larger data sets.

Root and Burnin

The root genome consisted of hg18 chr6:127,968,540-137,968,539 (10Mb) partitioned into two 5 Mb chromosomes with annotations populated from mgcGenes, knownGene, cpgIslandExt and ensGene tracks from the UCSC Table Browser. Details of infile set creation can be gleaned from the evolverInfileGeneration project

The root genome was evolved for a distance of 0.2 via 20 Evolver steps of 0.01, forming the simulation burnin. We used a much shorter initial burnin for this test simulation because this test set is intended to quickly iterate test evaluations and not make inferences. We wanted to make sure you could test evaluations using both the ancestor and root maf. The final genome of that burnin formed the ancestor for this simulation.

Tree

                ((simCow:0.18908,simDog:0.16303)sCow-sDog:0.032898,(simHuman:0.144018,(simMouse:0.084509,simRat:0.091589)sMouse-sRat:0.271974)sH-sM-sR:0.020593);

Summary Stats

Genome	Chr	Size (bp)
simCow	chr0	5,531,984
	chr1	5,521,188
	Total	11,053,172
simDog	chr0	5,470,523
	chr1	5,518,726
	Total	10,989,249
simHuman	chr0	5,417,450
	chr1	5,507,808
	Total	10,925,258
simMouse	chr0	5,686,491
	chr1	5,785,878
	Total	11,472,369
simRat	chr0	5,639,451
	chr1	5,701,332
	Total	11,340,783

Files

Script to download and create the correct directory structure: downloadTest.sh

An analysis package has the following directory structure:

packageTest/
              ..  README.txt
              ..  annotations/
              ..  predictions/
              ..  sequences/
              ..  truths/

These directories may be populated with the following (expand all files):

README.txt

annotations/

simTest.annots.tar.gz (16 MB)

version: 1

md5sum: 78e6dc3c21f842c38d2c8359e4962208

sha1sum: 90f58553a489e46095e415a992d31badf1e474e9

simTest.annots.gff.tar.gz (16 MB)

Annotations in gff format (optional).

version: 1

md5sum: a1df81a628c73e123cdcb1624bcccf64

sha1sum: 8a109c67e270d427595046ac2936e0d438fb1e9b

predictions/ - place your .maf files in here. Below is an example set of three mafs to play with.
- simTest.examplePredictions.tar.gz (95 MB)
```
version: 1
```
```
md5sum: 30f05c4868a530d1aa38824574a09e9d
```
```
sha1sum: 1ecab02b20ad3815152fa5c7ec2bdc78f913bd7b
```

sequences/

simTest.seqs.tar.gz (18 MB)

version: 1

md5sum: 579fbbfd2dfc8b07667eb0047d8a90da

sha1sum: b3da5a556626d4285698cedee0b71992e9234619

truths/ - the true mafs are placed in here
- Alignment to the MRCA, ancestor
  simTest.ancestor.maf.tar.gz (37 MB)
  
  aligns: {simMouse, simRat, sMouse-sRat, simHuman, sH-sM-sR, simCow, simDog, sCow-sDog, ancestor}
```
version: 1
```
```
md5sum: 5c73438007aef3cd255403e5ad4f5483
```
```
sha1sum: 1cc74062d03de0cb556795bb13d83f84e6a9d72c
```
- Alignment to the Root, root
  simTest.burnin.maf.tar.gz (48 MB)
  
  aligns: {simMouse, simRat, sMouse-sRat, simHuman, sH-sM-sR, simCow, simDog, sCow-sDog, ancestor, root}
```
version: 1
```
```
md5sum: 3fc9ff8328c3ed856a59a8235ccf0f5c
```
```
sha1sum: 16392bf7f360f45af220517a0bfcdb7318197beb
```
- Alignment to the MRCA and Root, with no paralogous blocks, ancestor.noparalogies, root.noparalogies
  simTest.noparalogiyMafs.tar.gz (82 MB)
  
  aligns: {simMouse, simRat, sMouse-sRat, simHuman, sH-sM-sR, simCow, simDog, sCow-sDog, ancestor, root}
```
version: 1
```
```
md5sum: 28fcdd2181ca095b66a73d674d355ae9
```
```
sha1sum: 6dad4195c444ed59c1e0e19857a45266b56561c8
```