Strandseq-InvertR Files

# README

# general notes on expected results:
# the example results illustrate the types of output files you can expect after running each example in the testData folder
# each run will generate:
	# a) individual subdirectories for each chromosome/ROI in the input.txt containing results for each library
	# b) WCLibs subdirectory that lists all libraries filtered based on the WCcutoff
	# c) overlaid histogram of all analyzed libraries
	# d) a summary read file (allFrequencies) that contains the read and deltaWC data for analyzed libraries
	# e) a summary ROI file (ROI_locations_Table) that contains putative inversion locations (if findROIs=T)
# IMPORTANT: Results depend on input bam files, and these expected results serve as a general guide
# to achieve these exact results contact administrator for the sample libraries used in this test
# Ashley D. Sanders


# notes on Example A. 

# no filtering is applied (WCcutoff=0) and all chromosomes are considered irrespective of the inheritance pattern (i.e. all ww, cc and wc chromosomes)
# putative inversions are not predicted (findROIs=F) and there is no ROI_locations_Table file generated



# notes on Example B. 

# filter is applied (default WCcutoff = 0.75) and only chromosomes passing the WCcutoff are analyzed (i.e. ww and cc chromosomes)
# if no chromsomes pass  filter summary files will be empty
# putative inversions are predicted (findROIs=T) and an ROI_locations_Table file is generated
# chromosomes containing SCEs can results in false calls and should be pre-filtered



# notes on Example c. 

# instead of whole chromosomes, targeted regions are analyzed to interrogate ROIs 
# not filtering is applied here (WCcutoff=0) all chromosomal regions are analyzed 
# putative inversions are predicted (findROIs=T) and an ROI_locations_Table file is generated
# chromosomes containing SCEs can results in false calls and should be pre-filtered