This directory contains a few Rscript files that constitute a first workflow for
analyzing the alignment files generated as recorded in the parent directory. The
scripts are meant to run in succession and can be invoked by the bash script

	./xrunwfHs all

In brief, *-wf1.Rscript sets up a TSSobject using the TSRchitect (Bioconductor)
R package; *-wf2.Rscript generates the TSS counts (TSSset-*.txt output),
explores summary statistics, and suggests thresholds for TSR determination
(*-wf2.out and *-wf2.pdf files); *-wf3.Rscript determines and outputs TSRs
(TSRset-*.tab and TSRset-*.txt files); and *-wf4.Rscript explores some genes of
interest (edit the list genesOfInterest in the script; output: *-wf4.out).

The Rscripts require various R packages. You can either install those packages
locally, or you can download our TSRchitect singularity container and run the
xrunwfHs script as follows:

	singularity pull --name tsr.simg shub://BrendelGroup/TSRchitect
	singularity exec -e -B ../ tsr.simg ./xrunwfHs all

Once you have the output of the Rscripts, you may want to inspect the output
data for obvious characteristics: how many TSRs have been predicted, how do they
match up with current gene annotation, what are the genes with strong promoter
usage, etc.. We provide the xexploreTSRset* scripts as templates for what can be
done easily without indepth analyis - try it, change it, do the indepth
analyses ...

Usage examples:
	xexploreTSRset TSRset-1.txt > explore-1.out
	xexploreTSRsetCombined TSRsetCombined.txt > explore-C.out
