From 8a6199b607c127484b64325c1d65f0970ca05b16 Mon Sep 17 00:00:00 2001 From: nservant <nicolas.servant@curie.fr> Date: Fri, 22 Jan 2021 21:53:46 +0100 Subject: [PATCH] [MODIF] edit README --- CHANGELOG.md | 5 +++++ README.md | 17 ++++++++++------- 2 files changed, 15 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6b38240..6eafbb3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.3.0dev - 2020-11-01 +* Add HiCExplorer distance decay quality control +* Add HiCExplorer TADs calling +* Add insulation score TADs calling +* Generate cooler/h5/txt contact maps +* Normalize Hi-C data with cooler instead of iced * New `--digestion` parameter to automatically set the restriction_site and ligation_site motifs * New `--keep_multi` and `keep_dup` options. Default: false * Template update for nf-core/tools v1.11 diff --git a/README.md b/README.md index 589bcb3..7be2010 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ ## Introduction -This pipeline is based on the +This pipeline was originally set up from the [HiC-Pro workflow](https://github.com/nservant/HiC-Pro). It was designed to process Hi-C data from raw FastQ files (paired-end Illumina data) to normalized contact maps. @@ -23,6 +23,8 @@ well as protocols that do not require restriction enzymes such as DNase Hi-C. In practice, this workflow was successfully applied to many data-sets including dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data. +Contact maps are generated in standard format including HiC-Pro, cooler, and h5 format. +Addition downstream analysis steps such as TADs calling are also available. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. @@ -32,13 +34,14 @@ results highly reproducible. ## Pipeline summary 1. Mapping using a two steps strategy to rescue reads spanning the ligation -sites (bowtie2) -2. Detection of valid interaction products +sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)) +2. Detection of valid interaction products([`HiC-Pro`](https://github.com/nservant/HiC-Pro)) 3. Duplicates removal -4. Create genome-wide contact maps at various resolution -5. Contact maps normalization using the ICE algorithm (iced) -6. Quality controls and report (MultiQC) -7. Addition export for visualisation and downstream analysis (cooler) +4. Create genome-wide contact maps at various resolution ([`cooler`](https://github.com/open2c/cooler)) +5. Contact maps normalization using the ICE algorithm ([`cooler`](https://github.com/open2c/cooler)) +6. Quality controls ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer)) +7. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooler`](https://github.com/open2c/cooler)) +8. Quality control report ([`MultiQC`](https://multiqc.info/)) ## Quick Start -- GitLab