In order to create a misha database for hg19 genome, run the following misha 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')
In order to create a misha database for hg38 genome, run the following misha commands (assuming "hg38" is your new data base path):
ftp <- "ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38" 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')
In order to create a misha database for mm9 genome, run the following misha 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')
In order to create a misha database for mm10 genome, run the following misha 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')
In order to import observed HiC contacts to an existing misha database (e.g. "hg19"):
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()
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