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# Snakemake workflow: chipseq
[![Snakemake](https://img.shields.io/badge/snakemake-≥6.4.0-brightgreen.svg)](https://snakemake.github.io)
[![GitHub actions status](https://github.com/snakemake-workflows/chipseq/workflows/Tests/badge.svg?branch=master)](https://github.com/snakemake-workflows/chipseq/actions?query=branch%3Amaster+workflow%3ATests)
This workflow is a Snakemake port of the [nextflow chipseq pipeline](https://nf-co.re/chipseq) and performs ChIP-seq peak-calling, QC and differential analysis.
......@@ -9,4 +8,15 @@ This workflow is a Snakemake port of the [nextflow chipseq pipeline](https://nf-
The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=snakemake-workflows/chipseq).
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).
# Credits
This template is derived from the official [Snakemake-workflow](https://github.com/snakemake-workflows/chipseq) by [Antonie Vietor](https://github.com/AntonieV) and [David Laehnemann](https://github.com/dlaehnemann).
Initially a port of the [Next-Flow ChIP-seq](https://nf-co.re/chipseq) (https://doi.org/10.5281/zenodo.3240506) by [Harshil Patel](https://github.com/drpatelh) [et al.](https://github.com/nf-core/chipseq/graphs/contributors)
## Main changes
- [Singularity](https://sylabs.io/singularity/) using a docker image publish on [Docker hub](https://hub.docker.com/r/ginolhac/snake-chip-seq)
- [AdapterRemoval](https://adapterremoval.readthedocs.io/en/latest/) for trimming (replacement of `cutadapt`)
- add [FastqScreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
......@@ -58,3 +58,10 @@ For each sample, add one or more sequencing units (runs or lanes) to the unit sh
| B | 1 | | | SRR1635457 | ILLUMINA |
| B | 2 | | | SRR1635458 | ILLUMINA |
| C | 1 | | | SRR1635439 | ILLUMINA |
# Interpreting outputs
See the page from the [nf-core](https://nf-co.re/chipseq/1.2.2/docs/output)
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