CaptureC analysis pipeline website

CaptureC analysis codes - CCanalyser, blat filtering, and statistics originally coded by James Davies.
Developed to more mature and pipelined format by Jelena Telenius.
Statistical analysis modified by Marieke Oudelaar, and Damien Downes.

Alpha testers (read "the heroes" ) : Joke Van Bemmel, Duantida Songdej, Damien Downes, Matthew Gosden, Mira Kassouf, Lars Hanssen, Ross Thorne
Beta testers : Jessica Davies, Anna Sanniti, Nigel Roberts, Nicolas Servant

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General documentation :

  1. What does the pipeline do ? - from input to output
  2. FAQ : Which pipeline version do I want to run ? - and why there is so many ?
  3. FAQ : What is the difference between VS05 and VS04 and VS03 ( CCseqBasic5/4/3 ) ?
  4. FAQ : Flashed and nonflashed reads - what is this ?
  5. FAQ : Blat - filtering, what is this ?
  6. FAQ : Ploidy - filtering, what is this ?
  7. FAQ : Duplicate - filtering, how does it differ from "normal duplicate filtering" ?
  8. FAQ : This is all very nice, but I would like to have more P-values here ?


Analysis workflow :

  1. Generate oligo coordinate file
  2. Run pipeline
  3. Interpret your results
  4. Normalise your tracks (compare between active and inactive tissue)
  5. Pool your samples (check that all your replicates look the same)
  6. Statistical analysis (get p-values for your comparison between active and inactive tissue)


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Oligo file generation instructions

updated by Jelena - 11:00 27/Feb/2017

Before you can start your pipeline run, you have to generate OLIGO COORDINATE file.

Oligo coordinate file has a very specific structure, described on step (13) here : User manual for CaptureC analysis without pipeline

To run the oligo-file generator scripts (below), you need :

  • List of your biotinylated capture oligos you used in your capture experiment
    • OR
  • MIG exported list of capture oligos (wig, bedgraph or tab format)

    • MIG-exported file is better - it will not contain "weird characters" like Excel files would.

    If you don't have the MIG exported file, you can make a file with Gedit in deva (command "gedit"), or with Comodo text editor (windows, mac - free download)
    Write the file like this : 
    chr11   32100432    32100532
chrX    15278946    15279030
    So, that is coordinates in a tab separated file (you don't need to name your oligos yet)


    Generating the file with automated scripts :

    1. run first part
      /t1-data/data/hugheslab/jelenatools/CC/oligoFileGenerator/firstPart.sh
    2. change oligo names (4th column) in the output file - if you want to name them "properly"
    3. run second part
      /t1-data/data/hugheslab/jelenatools/CC/oligoFileGenerator/secondPart.sh

    Help of the commands - just paste the command name (above)

    What do the above scripts do ?

    Back in the old days this step was done manually.
    These manual oligo file generation instructions will tell you what exactly the above scripts do for you :
    Generating_Oligo_Coordinate_File_For_CaptureC_analyser.pdf