data_sources.txt

# xgainsaw download template file
# 
# Each genome entry consists of Label, gDNA, Sizes, GFF, and Alias entries, representing
# respectively a name for the genome, a filename or URL for the genome sequence file, a
# UCSC style "genome file" giving the lengths of the genome sequences, a filename or URL
# for a corresponding (NCBI style) GFF annotation file, and a UCSC style Alias file
# converting NCBI sequence identifiers to UCSC identifiers.
#
# Please see the following example. Replace the comment line and second column entries
# appropriate for your upload needs.

# Usage: xgainsaw download -q mm39


# Mouse assembly version mm10
#
Label	mm10
gDNA	https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.fa.gz
Sizes	https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.chrom.sizes
Alias	https://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/chromAlias.txt.gz
Chain	https://hgdownload.soe.ucsc.edu/goldenPath/mm10/liftOver/mm10ToMm39.over.chain.gz

# Mouse assembly version mm39
#
Label	mm39
gDNA	https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz
Sizes	https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes
GFF	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.27_GRCm39/GCF_000001635.27_GRCm39_genomic.gff.gz
Alias	https://hgdownload.cse.ucsc.edu/goldenPath/mm39/database/chromAlias.txt.gz
Chain	https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToMm10.over.chain.gz
Chain	https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToRn7.over.chain.gz

# Rat assembly version rn7
#
Label	rn7
gDNA	https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.fa.gz
Sizes	https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.chrom.sizes
GFF	https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/227/675/GCF_015227675.2_mRatBN7.2/GCF_015227675.2_mRatBN7.2_genomic.gff.gz	
Alias	https://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.chromAlias.txt