Import

Netta Medndelson Cohen

2022-03-23

Source: vignettes/import.Rmd

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):

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 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')

mm9

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')

mm10

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')

Import HiC observed contacts

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

  1. 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.
  1. run the following misha command:
gsetroot("hg19")
gtrack.2d.import(track="hic_obs", description="observed hic data", file=c("hic.obs.txt"))
gdb.reload()