- You need these three scripts to run the analysis :
dpngenome3_1.pl (generates RE digestion fragments for your genome of interest)
dpnII2E.pl (generates RE digestion fragments for your sample)
CCanalyser2.pl (the master captureC analyser)
- The user manuals :
2a) WholeAnalysisPipelineUserManual.pdf
How to run the whole analysis, starting from fastq files and ending with ready-to-load visualisation files and run statistics. Includes instructions to modify the code to suit your own running environment, and a short trouble-shooting section.
2b) CCanalyser2_help_command_printout.pdf
Printout of the CCanalyser2.pl help command : lists available options and how to use the script. Use the above full pipeline manual along-side this listing, to troubleshoot your installation.