runInvertR: Wrapper function for InvertR
In drashley/InvertR: Finds putative inversions in Strand-seq sequencing data

Description Usage Arguments Details Author(s)

This script will move through .bam or .bed files in a folder and perform several steps (see Details).

runInvertR(regionTable, binSize = 50, WCcutoff = 0.75,
  dataDirectory = "./InvertR_analysis/", gapfile = 0, type = "bed",
  dup = TRUE, qual = 10, padding = 0, minDepth = 20, minReads = 20,
  verbose = TRUE, png = TRUE, strand = TRUE, ROI = FALSE,
  genotype = TRUE, findROIs = T)

`regionTable`	Genomic coordinates to be analyzed (ROI list or Chr Table)
`binSize`	The number of reads in each bin used to calculate wcRatio
`WCcutoff`	The number of watson or crick reads used to define chrStates
`dataDirectory`	Output directory. If non-existent it will be created
`gapfile`	Input txt file of gaps in the genome
`type`	File input type, either 'bed' or 'bam'
`dup`	If `TRUE`, removes duplicate reads
`qual`	Filter reads based on specified qulaity score
`padding`	Number of bases to extend beyond genomic coordinates listed in regionTable
`minDepth`	The minimum number of reads/Mb required to analyze the chromosome
`minReads`	The minimum number of reads within the ROI required for inclusion
`verbose`	If `TRUE` Verbose messages
`png`	If`TRUE` Generates a png figure of each file
`strand`	If `TRUE` Plot the crick and watson reads above the histrogram
`ROI`	If`TRUE` Expects ROI list, if`FALSE` Expects chromosome table
`findROIs`	If`TRUE` Runs findROIlocations to locate putative inversions

1. calculate the WCratio chromosome-by-chromosome 2. Locate the ROIs in chromosomes passing the WCcutoff 3. write a bedgraph file of wcRatios -> can upload on to UCSC Genome browser 4. write an ROI file for each index with all chromosomes included

Ashley D. Sanders, Mark Hills

drashley/InvertR documentation built on May 15, 2019, 1:54 p.m.