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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Interpret and troubleshoot analysis results !

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

1) Interpret your report file

These are instructions to interpret the output report counters :
Interpret your report file

These are instructions to the difference of "reads" and "fragments" in the report file :
Reads and fragments

Count the CIS and TRANS interactions (the above report does not divide the reporter fragments to cis and trans ):

/t1-data/data/hugheslab/jelenatools/CC/report/cis_trans_analyser.pl (copy of Marieke's script 27Feb2017)
and its current development version (in Marieke's folder) : /t1-data1/WTSA_Dev/oudelaar/scripts/cis_trans_analyser.pl 

Usage instructions :

# This script reads a gff file generated by CCanalyser and calcualtes the proportion of cis and trans interactions.
# Run with following options: -f full path to gff file -chr chromosome that is considered cis for this VP, eg chr11
# Example of a run command:
# perl /t1-data1/WTSA_Dev/oudelaar/scripts/cis_trans_analyser.pl -f /t1-data1/WTSA_Dev/oudelaar/ultra_vs_tagm/ultra_200/Rep1_S1_CC4/F6_greenGraphs_combined_ultra_rep1_CC4/COMBINED_CC4_Hba-1.gff -chr chr11

2) Oligo-file related issues

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

Back in the old days this step was done manually.
These manual oligo file generation instructions will tell you how to do this properly (out-house users cannot use autogenerators) :
Generating_Oligo_Coordinate_File_For_CaptureC_analyser.pdf

3) Pipeline manuals

There is no real manual at the time (10/Jan/2017) - but Jelena is writing one, the manual should be out around March 2017 !
Below some already-existing documentation, however !

These are instructions to interpret output, and better understand what the pipeline run does :
Interpret your results
- these instructions are a little outdated for CB4 and CC4 pipelines (red and orange graphs are not explained in the above).

These are instructions to run the steps of the pipeline one-by-one : they give a clear outline which tools form the "backbone" of the pipeline
User manual for CaptureC analysis without pipeline
- these instructions are a little outdated for CB4 and CC4 pipeline (red and orange graphs are not explained in the above) !

4) Deeper into the statistical analysis

Various ways tp get p-values for your data.

Statistical analysis with deSeq2, fourCSeq, r3CSeq

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