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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Statistics (compare inactive and active tissue)

updated by Jelena - 10:10 04/Jan/2018

Statistics pipeline - full statistics and visualisation, for 3 'condition' + 3 'control' samples

Bug fixes and updates (after release)

Current issues - known bugs and development targets !

Bug fixes and updates (old site)

Normalise to ALL READS (both cis and trans reads)

User instructions for CB3/CC3 pipeline output

User instructions for CB4/CC4/CF*/CS*/Cb* pipeline output

General user instructions for any CCanalyser.pl output - not ran via any Cx3/Cx4/Cx5 pipeline THIS USER CASE IS NOT BETA TESTED YET - report problems to Jelena if you encounter any !

Normalise to CIS ONLY (take into account only cis reads)

User instructions for CB3/CC3 pipeline output

User instructions for CB4/CC4/CF*/CS*/Cb* pipeline output

General user instructions for any CCanalyser.pl output - not ran via any Cx3/Cx4/Cx5 pipeline THIS USER CASE IS NOT BETA TESTED YET - report problems to Jelena if you encounter any !

Normalise your tracks (only visualisation) - normalising to ALL READS (both cis and trans reads)

Normalise your tracks (compare between active and inactive tissue)

Statistical analysis with deSeq2, fourCSeq, r3CSeq

Statistical analysis (get p-values for your comparison between active and inactive tissue)

Statistical analysis with Chicago, peakC, deSeq2, fourCSeq, r3CSeq

Statistical analysis (get p-values for your comparison between active and inactive tissue)