Keles -- Statistical Methods for profiling long range chromatin interactions from repetitive regions of the genome
- Multi-mapping reads (multi-reads) are typically thrown out in many HTS analyses incuding Hi-C
- Assays predominently rely on short-read (50-150bp) so multi-reads are common
- Using ChIP-seq as an example, incorporating multi-reads finds peaks in regions where "uni-reads" do not
- e.g. Perm-seq using DHS + ChIP-seq data and multi-reads. 27.3% more peaks compared to ENCODE uniform processing pipeline
- How to combine this with Hi-C data?
- Hi-C read processing
- Typical pipelines: singletons, multi-mapping ends, low map quality, and unaligned all discarded
- Hi-C read processing
- Evaluation of the impact of this using IMR90 and Plasmodium datasets