From df5a02432b256afc17009e86c08075ecdcc6e67c Mon Sep 17 00:00:00 2001 From: nservant <nicolas.servant@curie.fr> Date: Thu, 15 Apr 2021 10:09:56 +0200 Subject: [PATCH] [DOC] update README --- README.md | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 734275f..b211b5d 100644 --- a/README.md +++ b/README.md @@ -24,9 +24,9 @@ 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 formats including HiC-Pro, cooler, and h5 format for +Contact maps are generated in standard formats including HiC-Pro, and cooler for downstream analysis and visualization. -Addition analysis steps such as TADs calling are also available. +Addition analysis steps such as compartments and 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. @@ -35,15 +35,18 @@ results highly reproducible. ## Pipeline summary -1. Mapping using a two steps strategy to rescue reads spanning the ligation -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 ([`cooler`](https://github.com/open2c/cooler)) -5. Contact maps normalization using the ICE algorithm ([`cooler`](https://github.com/open2c/cooler)) -6. Export to various contact maps formats ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`cooler`](https://github.com/open2c/cooler), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer)) -7. Quality controls ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer)) -8. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooler`](https://github.com/open2c/cooler)) +1. HiC-Pro data processing [`HiC-Pro`](https://github.com/nservant/HiC-Pro) + 1. Mapping using a two steps strategy to rescue reads spanning the ligation + sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)) + 2. Detection of valid interaction products + 3. Duplicates removal + 4. Generate raw and normalized contact maps ([`iced`](https://github.com/hiclib/iced)) +2. Create genome-wide contact maps at various resolution ([`cooler`](https://github.com/open2c/cooler)) +3. Contact maps normalization using balancing algorithm ([`cooler`](https://github.com/open2c/cooler)) +4. Export to various contact maps formats ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`cooler`](https://github.com/open2c/cooler)) +5. Quality controls ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer)) +6. Compartments calling ([`cooltools`](https://cooltools.readthedocs.io/en/latest/)) +8. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooltools`](https://cooltools.readthedocs.io/en/latest/)) 9. Quality control report ([`MultiQC`](https://multiqc.info/)) ## Quick Start -- GitLab