From 8901a8e334f4410a149c354a43997d4c632933e3 Mon Sep 17 00:00:00 2001 From: nservant <nicolas.servant@curie.fr> Date: Fri, 22 Jan 2021 21:57:07 +0100 Subject: [PATCH] [MODIF] edit README --- README.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 7be2010..0c55644 100644 --- a/README.md +++ b/README.md @@ -23,8 +23,10 @@ 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. + +Contact maps are generated in standard format including HiC-Pro, cooler, and h5 format for +downstream analysis and visualization. +Addition 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. @@ -39,9 +41,10 @@ sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)) 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. 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/)) +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)) +9. Quality control report ([`MultiQC`](https://multiqc.info/)) ## Quick Start -- GitLab