Hosted here are analysis / processing methods for Chromatin Conformtion Capture (3C) experiments.
- Workflows:
- 3C processing (
./Ingest_3C
) - usesJuicer
for initial alignment/processing/normalization, then converts to.(m)cool
usinghic2cool
. First step to processing 3C data.
- 3C processing (
make_homer_input.sh
: Convert Juicer'smerged_nodup.txt
(or, really any file in AidenLab's "long" format) to a Homer-compatible format. This new input is then used to create a Tag Directory via Homer'smakeTagDirectory
.
- A series of R scripts mainly using the
GENOVA
package to do basic analyses and plot 3C data.
genova_loadCooler.R
- Load a .cool/.mcool file as a GENOVA-compatible object for plotting.
genova_viewMatrix.R
- Preconfigured GENOVA commands for viewing single & differential matrics in a variety of formats.
genova_aggregatePeakAnalysis.R
- Calculate APA values and plot.
FetchPixelFromMatrixGivenBedpe.py
: Given a matrix in.cool/.mcool
form and aBEDPE
file of interacting coordinates, extract raw and normalized contact counts.