Import

The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

Import

Netta Mendelson Cohen

2026-10-06

Create misha database from ucsc

hg19

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

url <- "https://hgdownload.soe.ucsc.edu/goldenPath/hg19/"
gdb.create("hg19",
           paste0(url, 'chromosomes/chr', c(1:22, 'X', 'Y', 'M'), '.fa.gz'),
           paste0(url, "database/knownGene.txt.gz"),
           paste0(url, "database/kgXref.txt.gz"),
           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 misha commands (assuming “hg38” is your new data base path):

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

mm9

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

url <- "https://hgdownload.soe.ucsc.edu/goldenPath/mm9/"
gdb.create("mm9",
           paste0(url, 'chromosomes/chr', c(1:19, 'X', 'Y', 'M'), '.fa.gz'),
           paste0(url, "database/knownGene.txt.gz"),
           paste0(url, "database/kgXref.txt.gz"),
           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 misha commands (assuming “mm10” is your new data base path):

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

Import HiC observed contacts

In order to import observed HiC contacts to an existing misha database (e.g. “hg19”):

create tab delimited text files (e.g. “hic.obs.txt”) with the following columns:

chrom1 - the first chromosome of the contact (must start with “chr”)
start1 - the first genomic coordinate
end1 - should be set to start1+1
chrom2 - the second chromosome of the contact (must start with “chr”)
start2 - the second genomic coordinate of the contact
end2 - should be set to start2+1
contacts - contains the number of reads found for this contact IMPORTANT NOTES: misha uses 0-based coordinates! File must contain a header line with the following columns: chrom1, start1, end1, chrom2, start2, end2, contacts in this order. Coordinates must be unique - cannot have the same contact more than once.

run the following misha command:

gsetroot("hg19")
gtrack.2d.import(track="hic_obs", description="observed hic data", file=c("hic.obs.txt"))
gdb.reload()

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.