lincRNA README.

Assumption.

1. Samples have been run through MAPRSeq workflow.
2. MAPRSeq workflow results have been delivered.

Assumption workaround.

1.a: If Samples are from external source and aligned BAM files are available.
	 lincRNA workflow can be fooled by creating a MAPRSeq directory strucuture and
	 adding respective files to approprite folders.

2.a: Be sure that results are delivered.  If MAPRSeq workflow results are not delivered
	 lincRNA may overwrite some of the existing files in secondary folder structure.


Run lincRNA workflow.

	1. Setup config files.

		1.a. Append lincRNA essentail config files to respective config files from MAPRSeq.
			 i. Since lincRNA is an extension to MAPRSeq and utilizes MAPRSeq workflow, scripts
			 this is required.

			 ii. There is a merged tool and memory info config files available under config folder
			 if required.

			 iii.  Complete example of all config files are available in "config" dir to be copied over
			 for your execution.


	2. Confirm that aligned BAM files are in folder structred as described by MAPRSeq.

	3. To execute workflow
		/data2/bsi/staff_analysis/m101236/codebase/lincRNA/lincRNA.pl -r=/complete/path/to/run_info.txt
