Homo sapiens - hg19 - refseq_r45 - v9 databases - Gene based

• rankings: Matrix containing motifs as rows and genes as columns and ranking position for each gene and motif (based on CRM scores) as values. To be used with cisTarget (R).

• 500bpUp: 500bp upstream of TSS.
• TSS+/-10kb: 10kb around the TSS (total: 20kb).
• TSS+/-5kb: 5kb around the TSS (total: 10kb).

# Specify database:
feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-500bp-upstream-7species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-500bp-upstream-10species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-5kb-7species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-5kb-10species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-10kb-7species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather'
# Download database with zsync_curl:
"${ZSYNC_CURL}" "${feather_database_url}.zsync"

# Specify database:
feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-500bp-upstream-7species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-500bp-upstream-10species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-5kb-7species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-5kb-10species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-10kb-7species.mc9nr.genes_vs_motifs.rankings.feather'
# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather'
feather_database="${feather_database_url##*/}"

# Download database directly (with wget or curl):
wget "${feather_database_url}"
# curl -O "${feather_database_url}"

# Download sha256sum.txt (with wget or curl):
wget https://resources.aertslab.org/cistarget/databases/sha256sum.txt
# curl -O https://resources.aertslab.org/cistarget/databases/sha256sum.txt

# Check if sha256 checksum matches for the downloaded database:
awk -v feather_database=${feather_database} '$2 == feather_database' sha256sum.txt | sha256sum -c -

# If you downloaded mulitple databases, you can check them all at onces with:
sha256sum -c sha256sum.txt

	Name	Last modified	Size	Description
	Parent Directory		-
	hg19-500bp-upstream-7species.mc9nr.genes_vs_motifs.rankings.feather	2022-06-29 15:08	1.0G
	hg19-500bp-upstream-7species.mc9nr.genes_vs_motifs.rankings.feather.sha1sum.txt	2022-10-10 14:14	110
	hg19-500bp-upstream-10species.mc9nr.genes_vs_motifs.rankings.feather	2022-06-29 15:09	1.0G
	hg19-500bp-upstream-10species.mc9nr.genes_vs_motifs.rankings.feather.sha1sum.txt	2022-10-10 14:14	111
	hg19-tss-centered-5kb-7species.mc9nr.genes_vs_motifs.rankings.feather	2022-06-29 15:07	967M
	hg19-tss-centered-5kb-7species.mc9nr.genes_vs_motifs.rankings.feather.sha1sum.txt	2022-10-10 14:14	112
	hg19-tss-centered-5kb-10species.mc9nr.genes_vs_motifs.rankings.feather	2022-06-29 15:08	963M
	hg19-tss-centered-5kb-10species.mc9nr.genes_vs_motifs.rankings.feather.sha1sum.txt	2022-10-10 14:14	113
	hg19-tss-centered-10kb-7species.mc9nr.genes_vs_motifs.rankings.feather	2022-06-29 15:08	961M
	hg19-tss-centered-10kb-7species.mc9nr.genes_vs_motifs.rankings.feather.sha1sum.txt	2022-10-10 14:14	113
	hg19-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather	2022-06-29 15:07	958M
	hg19-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather.sha1sum.txt	2022-10-10 14:14	114