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

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)

This page updated by Jelena - 11:40 11/Jun/2018
(most above pages are updated more often than this main page)