## Create minimal example GFF/GTF files.
##
## Note that these commands are memory hungry and don't always work well on a
## low power virtual machine.
##
## Refer to koopa `download-gtf.sh` for URLs.
##
## Set the working directory to script path.
library(R.utils)
## Ensembl GRCh38 GTF ====
download.file(
url = pasteURL(
"ftp.ensembl.org",
"pub",
"release-95",
"gtf",
"homo_sapiens",
"Homo_sapiens.GRCh38.95.gtf.gz",
protocol = "ftp"
),
destfile = "ensembl.gtf.gz"
)
gunzip("ensembl.gtf.gz", remove = FALSE, overwrite = TRUE)
## Note that this manual cutoff can create issues with TxDb checks.
system("head -n 1000 ensembl.gtf > ensembl_head.gtf")
file.rename("ensembl_head.gtf", "ensembl.gtf")
gzip("ensembl.gtf", overwrite = TRUE)
## Ensembl GRCh38 GFF3 ====
download.file(
url = pasteURL(
"ftp.ensembl.org",
"pub",
"release-95",
"gff3",
"homo_sapiens",
"Homo_sapiens.GRCh38.95.gff3.gz",
protocol = "ftp"
),
destfile = "ensembl.gff3.gz"
)
gunzip("ensembl.gff3.gz", remove = FALSE, overwrite = TRUE)
system("head -n 1000 ensembl.gff3 > ensembl_head.gff3")
file.rename("ensembl_head.gff3", "ensembl.gff3")
gzip("ensembl.gff3", overwrite = TRUE)
## GENCODE GRCh38 GTF ====
download.file(
url = pasteURL(
"ftp.ebi.ac.uk",
"pub",
"databases",
"gencode",
"Gencode_human",
"release_29",
"gencode.v29.annotation.gtf.gz",
protocol = "ftp"
),
destfile = "gencode.gtf.gz"
)
gunzip("gencode.gtf.gz", remove = FALSE, overwrite = TRUE)
system("head -n 1000 gencode.gtf > gencode_head.gtf")
file.rename("gencode_head.gtf", "gencode.gtf")
gzip("gencode.gtf", overwrite = TRUE)
## GENCODE GRCh38 GFF3 ====
download.file(
url = pasteURL(
"ftp.ebi.ac.uk",
"pub",
"databases",
"gencode",
"Gencode_human",
"release_29",
"gencode.v29.annotation.gff3.gz",
protocol = "ftp"
),
destfile = "gencode.gff3.gz"
)
gunzip("gencode.gff3.gz", remove = FALSE, overwrite = TRUE)
system("head -n 1000 gencode.gff3 > gencode_head.gff3")
file.rename("gencode_head.gff3", "gencode.gff3")
gzip("gencode.gff3", overwrite = TRUE)
## RefSeq GRCh38.p12 GTF ====
download.file(
url = pasteURL(
"ftp.ncbi.nlm.nih.gov",
"genomes",
"refseq",
"vertebrate_mammalian",
"Homo_sapiens",
"reference",
"GCF_000001405.38_GRCh38.p12",
"GCF_000001405.38_GRCh38.p12_genomic.gtf.gz",
protocol = "ftp"
),
destfile = "refseq.gtf.gz"
)
gunzip("refseq.gtf.gz", remove = FALSE, overwrite = TRUE)
system("head -n 1000 refseq.gtf > refseq_head.gtf")
file.rename("refseq_head.gtf", "refseq.gtf")
gzip("refseq.gtf", overwrite = TRUE)
## RefSeq GRCh38.p12 GFF3 ====
download.file(
url = pasteURL(
"ftp.ncbi.nlm.nih.gov",
"genomes",
"refseq",
"vertebrate_mammalian",
"Homo_sapiens",
"reference",
"GCF_000001405.38_GRCh38.p12",
"GCF_000001405.38_GRCh38.p12_genomic.gff.gz",
protocol = "ftp"
),
destfile = "refseq.gff.gz"
)
gunzip("refseq.gff.gz", remove = FALSE, overwrite = TRUE)
system("head -n 1000 refseq.gff > refseq_head.gff")
file.rename("refseq_head.gff", "refseq.gff")
gzip("refseq.gff", overwrite = TRUE)
## FlyBase GTF ====
download.file(
url = pasteURL(
"ftp.flybase.net",
"releases",
"FB2018_05",
"dmel_r6.24",
"gtf",
"dmel-all-r6.24.gtf.gz",
protocol = "ftp"
),
destfile = "flybase.gtf.gz"
)
gunzip("flybase.gtf.gz", remove = FALSE, overwrite = TRUE)
system("head -n 1000 flybase.gtf > flybase_head.gtf")
file.rename("flybase_head.gtf", "flybase.gtf")
gzip("flybase.gtf", overwrite = TRUE)
## WormBase GTF ====
download.file(
url = pasteURL(
"ftp.wormbase.org",
"pub",
"wormbase",
"releases",
"WS268",
"species",
"c_elegans",
"PRJNA13758",
"c_elegans.PRJNA13758.WS268.canonical_geneset.gtf.gz",
protocol = "ftp"
),
destfile = "wormbase.gtf.gz"
)
gunzip("wormbase.gtf.gz", remove = FALSE, overwrite = TRUE)
system("head -n 1000 wormbase.gtf > wormbase_head.gtf")
file.rename("wormbase_head.gtf", "wormbase.gtf")
gzip("wormbase.gtf", overwrite = TRUE)
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