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# Snakemake workflow: chipseq
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This workflow is a Snakemake port of the [nextflow chipseq pipeline]( 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](
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]( by [Antonie Vietor]( and [David Laehnemann](
Initially a port of the [Next-Flow ChIP-seq]( ( by [Harshil Patel]( [et al.](
## Main changes
- [Singularity]( using a docker image publish on [Docker hub](
- [AdapterRemoval]( for trimming (replacement of `cutadapt`)
- add [FastqScreen](
......@@ -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](
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