dmr_gene_annotation

Cleans reference file and creates genomic region files (TSS, geneBody, TES, 5dist, and intergenic) from the reference.

Required Arguments

  • -r file or --referenceFile file: Reference file.

  • -g file or --genomeFile file: Genome file, with one column containing chromosome names and another column containing the length of each chromosome.

  • -hu y/m/r or --human y/m/r: Is the sample from a human? Use yes/y for human, mouse/m for mouse, or rat/r for rat. If not, it must be from either the mouse (m) or rat (r) genome.

  • -n y/n or --numericalChr y/n: Will you operate with numerical chromosome names or not? Use yes/y if using numerical chromosome names or no/n if using alphanumeric names. The choice must match the chromosome naming convention in the genomeFile. The default is no.

Optional Arguments

  • -rm or --removeMir: Remove genes with names starting with ‘Mir’? Use yes/y or no/n. The default is yes.

  • -X: The number of upstream base pairs (bp) for TSS, TES, and genes. The default is 1000.

  • -Y: The number of downstream base pairs (bp) for TSS, TES, and genes. The default is 1000.

  • -M: The number of base pairs (bp) from the gene start site for the 5dist region. The default is 10000.

  • -N: The number of base pairs (bp) from the gene start site for the 5dist region. The default is 1000000.

  • -i or --intergenicBTGenes: Are intergenic regions between gene body regions (yes/y) or between TSS and TES regions (no/n)? The default is yes.

  • -l or --minIntergenicLen: The minimum intergenic region distance. The default is 2000.

  • -xL or --maxIntergenicLen: The maximum intergenic region distance. The default is 10000000.

  • -rem or --removeShort: Should regions be removed from TSS, TES, and 5dist regions if the gene body is removed due to its size being less than 0? Use yes/y or no/n. The default is yes.

  • -F or --folderOut: The name of the output folder. The default is “out”.