updated by Jelena - 14:10 14/Jun/2017

Send all confusion and weird things to jelena__telenius__at__gmail__com

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Statistics script

BUGS / NON-STANDARD BEHAVIOR :

DEseq2 crashes still crash DEseq2 analysis for ALL subsequent oligos
( not only the oligo which crashed ).
These are mostly harmless crashes (DEseq2 cannot see any difference between profiles, and reports "empty", which crashes the script).
To run this kind of samples : take out the oligo(s) which crash the DEseq2, and run the script again.
Annoyingly manual way to run it, but possible.


INSTABILITY ISSUES :

Does not kill the script properly when any of the underlying scripts fail.
Only checks for output files, and not even that for the last script (CCanalyser).

DEVELOPMENT TARGETS (only Pipe2 is developed) :

1) Better crashing behavior - crashes when any of the perl scripts crashes.
2) Input format integrity testing - not allowing any of the files to go to next steps if they are not of proper format
3) Deleting files when they are not any more needed (currently saves all files from FLASHing step onwards)

4) Organising output folders for easy input to FourCSeq, PeakC, r3Cseq (possibly generating pre-input files for these in output)
5) Keeping track who is running and if the run crashed