Benjamin Langmead BenLangmead

## GLBio_3D.md

      
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                Notes for 3D genome track at GLBio 2017
              
          
    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


Evaluation of the impact of this using IMR90 and Plasmodium datasets