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All_networks.readme.txt
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# Chromatin assortativity analysis
# Based on Pancaldi et al, 2016
# With new chromatin features and networks by Kat Cheung
######################################################################################################################
# Original analysis:
# Original figshare page from Vera: https://figshare.com/articles/ChromatinAssortativity/2009232/7
# Github of cleaned up script and data using mESC PCHiC network: https://github.com/ricolab/Chromatin_Assortativity
# Alignment files in bam format for ChIP-seq features (new and old) are here: /data/data_public/Alignments_mESCs
# Original features were from Juan et al
# Vera's scripts and data can be found in figshare as well as: /data/Projects/kat/Projects/Assortativity
# My version of Vera's scripts are in /data/Projects/kat/Projects/Assortativity/ChAs_collated.R
# Original plots from Vera's paper I re-generated: /data/Projects/kat/Projects/Assortativity/figures
######################################################################################################################
# New analysis incorporating new ChIP-seq features and orignal networks from paper
# My scripts are in /home/kat/Repos/
# mESC PCHiC and HiCap and CHIA-PET networks (from Vera's paper)
# Assortavity plots generated with new features - H3K9me2, DNMTs, INO80 (and INO80_state), DRIP-Seq etc
# Original features and new features were binarised together, original features were binarised using an older version of
# ChromHMM (with different reference genome version) so I binarised them again using ChromHMM version 1.12
# Process new features: /home/kat/Repos/Assortativity/ChAs_new/scripts/process_new_binarised_data.r
# plots here: /home/kat/Repos/Assortativity/ChAs_new/figures
######################################################################################################################
# DnaseI capture Hi-C in mESC
# Interaction map here: /data/Projects/kat/Projects/Assortativity_new/new_networks/DnaseI_capture_hic/GSE72164_Hi-C_Merged_interactions_intervals.txt
# Use interactions > 5 in serum grown mESCs (cells used for ChIP-seq were also grown in serum)
# Initial DnaseI network processing: /home/kat/Repos/Assortativity/ChAs_new/scripts/dnaseI_ChAs.r
# DnaseI network was initially subdivided by accessible - accessible and accessible - inaccessible interactions
# Subdividing DnaseI network by chromatin state interactions
# mESC chromatin states (segments with posterior probability > 0.95) from Juan et al
# Data here: /data/Projects/kat/Projects/Assortativity_new/mESC_chromatin_states/mESC_chrom_states_95.txt
# Fragments are assigned a chromatin state if > 50% of that fragment overlaps a specific state
# Script here: /home/kat/Repos/Assortativity/ChAs_new/mESC_chromatin_states_ChAs/DnaseI_chromatin_states/mESCs_chromatin_states.r
# plots here: /home/kat/Repos/Assortativity/ChAs_new/mESC_chromatin_states_ChAs/DnaseI_chromatin_states/AcAc_AcIn/
# PCA and clustering
# PCA of DnaseI subnetworks (and features) using matrix of assortativity
# Script here: /home/kat/Repos/Assortativity/ChAs_new/scripts/ChAs_biclust_dnaseI_subnetworks.r
######################################################################################################################
# mESC cohesin and oct4 HiChip
# Not analysed using Chicago
# Results very similar betweeen the two HiChIPs, potentially they need to be re-analysed
# Script here: /home/kat/Repos/Assortativity/ChAs_new/scripts/
######################################################################################################################
# Human monocyte and neutrophil PCHiC
# PCHiC networks here: /mnt/nocode/data_public/pchic_interaction_networks
# Transcription factor ChIP-seq from Sanger
# Bam files here: /data/data_private/WP10x/monoctye_neutrophil_bam
# Script here: /home/kat/Repos/Assortativity/ChAs_new/WP10x_monocyte_neutrophil/WP10x_monocyte_neutrophil/scripts/process_binarised_data.r
# Plots here: /home/kat/Repos/Assortativity/human_monocyte_neutrophil_ChAs/
######################################################################################################################
# HeLa cells RNAPII and CTCF CHIA-PET
# CHIA-PET interactions were lifted over from hg19 to hg38
# Liftover script here: /home/kat/Repos/Assortativity/HeLa_ChiaPet_liftover.sh
# Liftover tool here: /data/Projects/kat/Tools/UCSC_liftOver/
# Using ChIP-seq data from John Higgins' group (mitotic and asynchronous) and also downloaded from ENCODE (asynchronous by default)
# 3 different ChromHMM binarisation runs, combine these in R
# Script here: /home/kat/Repos/Assortativity/HeLa_binarised_data_ChAs.r