###############################################################################
  ALEA: Toolbox for allele-specific epigenomcis analysis
  Mouse test data
###############################################################################


> ls -go test-data/mouse/

-rw-r--r-- 1        441 Aug 20 15:35 C57BL6J.fasta.refmap
-rw-r--r-- 1  562442894 Aug 20 11:57 H3K36me3.fastq.gz
-rw-r--r-- 1  688377229 Aug 26 17:29 mgp.v2.indels.chrname.vcf.gz
-rw-r--r-- 1    1769414 Aug 26 17:29 mgp.v2.indels.chrname.vcf.gz.tbi
-rw-r--r-- 1 5580872284 Aug 26 17:31 mgp.v2.snps.chrname.vcf.gz
-rw-r--r-- 1    2279428 Aug 26 17:31 mgp.v2.snps.chrname.vcf.gz.tbi
-rw-r--r-- 1 2688098092 Aug 26 17:34 mm9_build37_mouse.fasta
-rw-r--r-- 1        689 Aug 26 17:34 mm9_build37_mouse.fasta.fai
-rw-r--r-- 1        331 Aug 19 15:05 mm9.fullchrom.sizes
-rw-r--r-- 1       4719 Aug 27 12:06 README.txt


###############################################################################
  H3K36me3.fastq.gz
###############################################################################

The H3K36me3 data is obtained from:
Calabrese JM, Sun W, Song L, Mugford JW et al. "Site-specific silencing of
regulatory elements as a mechanism of X inactivation".
Cell 2012 Nov 21;151(5):951-63. PMID: 23178118
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM967646

SRA files were downloaded from
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX%2FSRX160%2FSRX160404/SRR522267/SRR522267.sra
on 2/15/2013 and converted to fastq using SRA toolkit:

> fastq-dump -A H3K36me3 ./SRR522267.sra
> gzip H3K36me3.fastq


###############################################################################
  mgp.v2.indels.chrname.vcf.gz
  mgp.v2.indels.chrname.vcf.gz.tbi
  mgp.v2.snps.chrname.vcf.gz
  mgp.v2.snps.chrname.vcf.gz.tbi
###############################################################################

The original SNPs and indels vcf files were obtained from the Sanger Institute
on 2/15/2013. ftp url:
ftp://ftp-mouse.sanger.ac.uk/REL-1211-SNPs_Indels/
The chromosome names are modified to include "chr" running the
following commands:

> gunzip -c mgp.v2.snps.annot.reformat.vcf.gz > mgp.v2.snps.annot.reformat.vcf
> cat mgp.v2.snps.annot.reformat.vcf | awk '{print "chr"$0}' | sed 's/chr#/#/g' > mgp.v2.snps.chrname.vcf
> bgzip mgp.v2.snps.chrname.vcf
> tabix -p vcf mgp.v2.snps.chrname.vcf.gz

> gunzip -c mgp.v2.indels.annot.reformat.vcf.gz > mgp.v2.indels.annot.reformat.vcf
> cat mgp.v2.indels.annot.reformat.vcf | awk '{print "chr"$0}' | sed 's/chr#/#/g' > mgp.v2.indels.chrname.vcf
> bgzip mgp.v2.indels.chrname.vcf
> tabix -p vcf mgp.v2.indels.chrname.vcf.gz


###############################################################################
  mm9_build37_mouse.fasta
  mm9_build37_mouse.fasta.fai
###############################################################################

The mouse reference genome NCBI build 37 (mm9), with the chromosome names
changed to the following:
chr1 through chr 19, chrM chrX and chrY

> cat mm9_build37_mouse.fasta.fai

chr1	197195432	6	80	81
chr10	129993255	199660388	80	81
chr11	121843856	331278566	80	81
chr12	121257530	454645478	80	81
chr13	120284312	577418735	80	81
chr14	125194864	699206608	80	81
chr15	103494974	825966415	80	81
chr16	98319150	930755084	80	81
chr17	95272651	1030303231	80	81
chr18	90772031	1126766798	80	81
chr19	61342430	1218673487	80	81
chr2	181748087	1280782704	80	81
chr3	159599783	1464802649	80	81
chr4	155630120	1626397436	80	81
chr5	152537259	1783972939	80	81
chr6	149517037	1938416920	80	81
chr7	152524553	2089802926	80	81
chr8	131738871	2244234042	80	81
chr9	124076172	2377619655	80	81
chrM	16299	2503246786	70	71
chrX	166650296	2503263324	80	81
chrY	15902555	2671996755	80	81


###############################################################################
  mm9.fullchrom.sizes
###############################################################################

Contains chromosome sizes required to create final BigWig tracks:

> cat mm9.fullchrom.sizes

chr1	197195432
chr2	181748087
chr3	159599783
chr4	155630120
chr5	152537259
chr6	149517037
chr7	152524553
chr8	131738871
chr9	124076172
chr10	129993255
chr11	121843856
chr12	121257530
chr13	120284312
chr14	125194864
chr15	103494974
chr16	98319150
chr17	95272651
chr18	90772031
chr19	61342430
chrX	166650296
chrY	15902555
chrM	16300