Perform simple/twisted analysis for promoter capture Hi-C analysis

TheJacksonLaboratory / diachromatic

Diachromatic is a Java application for preprocessing and quality control of Hi-C and CHi-C data.

https://diachromatic.readthedocs.io/en/latest/

GNU General Public License v3.0

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Closed hansenp closed 5 years ago

hansenp commented 5 years ago

We will use the data of Mifsud et al. 2015 that can be found here:

/projects/robinson-lab/hansenp/captureCpipeline/hicup_pipeline/data/mifsud_et_al_2015/

[ ] Perform primary analysis with Diachromatic
[ ] Apply pipeline of Jonas to interaction data
[ ] Perform analysis with significance of directed k-interactions
[ ] Perform motif analysis simple vs twisted, twisted vs simple, simple vs undirected, twisted vs undirected on filtered interactions