A set of tools for Hi-C data analysis developed by Bioinformatics and Machine Learning Lab
- Attached are the chromatin state bed files. We have 10 states for young and old (O_E1, O_E2, etc; O_E1 means chromatin state 1 in old MuSCs), there is genome location information in each file, could you calculate the contact frequency for each state? I can put this Hic contact information on ChromHMM analysis.
- Could you give us some examples to show the visualization for enhancer-related differential loops on the genome browser and HiC maps? I already send some regions to you. I will have a presentation next Wednesday in our LGG meeting, if you can give this before Wednesday, that would be great.
- You can do some analysis to show what’s the difference with age at compartment, TAD, and loop levels. I attached the pre-published paper here, you can look at Fig6.
- Files to visualize arcs in UCSC genome browser
- Some basic QC with the HiC data to include in Supplement
- PCA of compartments, TADs and loops