What are the parameters in the command ?

The common 'top folder' of all the folders :

    --path /t1-data/usr/....../Promoter_capture

The CCanalyser version :

    --ccversion CC3

The folder names of the samples - subfolders (F6) don't need to be mentioned, as it is CC4 run, the script knows to go into F6 folder !

    --folders Analysis_INSERT_EB5,Analysis_INSERT_EB6,Analysis_INSERT_EB7,Analysis_WT_Sp5,Analysis_WT_Sp6,Analysis_WT_Sp15

The identifier of the "CONDITION" samples - part of the folder name unique to these 3 replicates

    --condition INSERT

The identifier of the "CONTROL" samples - part of the folder name unique to these 3 replicates

    --control WT

Then you need to add the other parameters :

Which genome you mapped to in your CCanalyser.pl ?

    --genome mm9

Where you want your data to be stored in your public area ? (this folder does not need to exist)

    --pf /public/username/capturedata/analysis

What do you want your output folder and data hub to be called ?

    --name myAnalysis

Which are your genes of interest ? (these are names from the oligo coordinate file - except for combined globines you need to check the output gff name separately)

    --genes Mitof,SOX2,nanog