Statistics (compare inactive and active tissue) for CC3 pipeline output

Bug fixes and updates (after release)

Bug reports (not yet fixed)

You need 3 replicates in both 'condition' and 'control' samples - somewhere in /t1-data/ or /t1-data1/ area.

EXAMPLE INPUT FOLDER - any output data from six runs (six samples = 3 'condition' + 3 'control' ) with CCanalyser2.pl script

All the output data is in same folder
located in /t1-data/usr/....../Promoter_capture

Promoter_capture
   |
   | CONDITION-samples (3 replicates)
   |
   |-- Analysis_INSERT_EB5
   |   `-- CCanalyser_gff_files_of_INSERT_EB5
   |        |-INSERT_EB5_Mitof.gff
   |        |-INSERT_EB5_SOX2.gff
   |        `-INSERT_EB5_nanog.gff
   |
   |-- Analysis_INSERT_EB6
   |   `-- CCanalyser_gff_files_of_INSERT_EB6
   |-- Analysis_INSERT_EB7
   |   `-- CCanalyser_gff_files_of_INSERT_EB7
   |
   | CONTROL-samples (3 replicates)
   |
   |-- Analysis_WT_Sp5
   |   `-- CCanalyser_gff_files_of_WT_Sp5
   |-- Analysis_WT_Sp6
   |   `-- CCanalyser_gff_files_of_WT_Sp6
   `-- Analysis_WT_Sp15
       `-- CCanalyser_gff_files_of_WT_Sp15

RUN COMMAND for the above input folder

    
/t1-data/data/hugheslab/jelenatools/CC/statisticsCis/statisticsRunner.sh 
    --genome mm9
    --pf /public/username/capturedata/analysis
    --condition INSERT 
    --control WT
    --name myAnalysis 
    --path /t1-data/usr/....../Promoter_capture 
    --nonPipelineFolders Analysis_INSERT_EB5/CCanalyser_gff_files_of_INSERT_EB5,Analysis_INSERT_EB6/CCanalyser_gff_files_of_INSERT_EB6,Analysis_INSERT_EB7/CCanalyser_gff_files_of_INSERT_EB7,Analysis_WT_Sp5/CCanalyser_gff_files_of_WT_Sp5,Analysis_WT_Sp6CCanalyser_gff_files_of_WT_Sp6,Analysis_WT_Sp15/CCanalyser_gff_files_of_WT_Sp15 
    --oligos Mitof,SOX2,nanog
    --oligoFile /full/path/to/usedOligoFile.txt ( should contain AT LEAST the oligos listed in --oligos above )

What are the above parameters ???

How to start run with the above command ?

If you are in your top folder /t1-data/usr/....../Promoter_capture :

All oligos in correct format :

cat Analysis_INSERT_EB5/usedOligoFile.txt | sed 's/\s.*//' | tr "\n" "," | sed 's/,$//' | awk '{print $0}'

NOTE !!
If you combined your globins, the combined oligo names will not be in your oligo file !
Add to the oligo file one line for HbaCombined and one line for HbbCombined.
The code only needs the column "chr" - to determine which chromosome is cis. Other columns can be empty.
Add to your oligo list the combined globin names :
--oligos mpg,nprl3,HbaCombined,HbbCombined

RUN SCRIPT