Genomes

library(misha)

Create a misha database from UCSC

hg19

In order to create a misha database for hg19 genome, run the following commands (assuming “hg19” is your new data base path):

ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19"
gdb.create(
    "hg19",
    paste(ftp, "chromosomes", paste0("chr", c(1:22, "X", "Y", "M"), ".fa.gz"), sep = "/"),
    paste(ftp, "database/knownGene.txt.gz", sep = "/"),
    paste(ftp, "database/kgXref.txt.gz", sep = "/"),
    c(
        "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol",
        "refseq", "protAcc", "description", "rfamAcc",
        "tRnaName"
    )
)
gdb.init("hg19")

hg38

In order to create a misha database for hg38 genome, run the following commands (assuming “hg38” is your new data base path):

ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38"
gdb.create(
    "hg38",
    paste(ftp, "chromosomes", paste0("chr", c(1:22, "X", "Y", "M"), ".fa.gz"), sep = "/"),
    paste(ftp, "database/knownGene.txt.gz", sep = "/"),
    paste(ftp, "database/kgXref.txt.gz", sep = "/"),
    c(
        "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol",
        "refseq", "protAcc", "description", "rfamAcc",
        "tRnaName"
    )
)
gdb.init("hg19")

mm9

In order to create a misha database for mm9 genome, run the following commands (assuming “mm9” is your new data base path):

ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9"
gdb.create(
    "mm9",
    paste(ftp, "chromosomes", paste0("chr", c(1:19, "X", "Y", "M"), ".fa.gz"), sep = "/"),
    paste(ftp, "database/knownGene.txt.gz", sep = "/"),
    paste(ftp, "database/kgXref.txt.gz", sep = "/"),
    c(
        "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol",
        "refseq", "protAcc", "description"
    )
)
gdb.init("mm9")

mm10

In order to create a misha database for mm10 genome, run the following commands (assuming “mm10” is your new data base path):

ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10"
gdb.create(
    "mm10",
    paste(ftp, "chromosomes", paste0("chr", c(1:19, "X", "Y", "M"), ".fa.gz"), sep = "/"),
    paste(ftp, "database/knownGene.txt.gz", sep = "/"),
    paste(ftp, "database/kgXref.txt.gz", sep = "/"),
    c(
        "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol",
        "refseq", "protAcc", "description", "rfamAcc",
        "tRnaName"
    )
)
gdb.init("mm10")

mm39

In order to create a misha database for mm39 genome, run the following commands (assuming “mm39” is your new data base path):

ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39"
gdb.create(
    "mm39",
    paste(ftp, "chromosomes", paste0("chr", c(1:19, "X", "Y", "M"), ".fa.gz"), sep = "/"),
    paste(ftp, "database/knownGene.txt.gz", sep = "/"),
    paste(ftp, "database/kgXref.txt.gz", sep = "/"),
    c(
        "kgID", "mRNA", "spID", "spDisplayID", "geneSymbol",
        "refseq", "protAcc", "description", "rfamAcc",
        "tRnaName"
    )
)
gdb.init("mm39")