This workflow takes as input a collection of paired fastqs. Remove adapters with cutadapt, map pairs with bowtie2. Keep MAPQ30 and concordant pairs. MACS2 for paired bam.

This workflow takes as input a collection of fastqs (single reads). Remove adapters with cutadapt, map with bowtie2. Keep MAPQ30. MACS2 for bam with fixed extension or model.

prepareChIPs

This is a simple snakemake workflow template for preparing single-end ChIP-Seq data. The steps implemented are:

1. Download raw fastq files from SRA
2. Trim and Filter raw fastq files using AdapterRemoval
3. Align to the supplied genome using bowtie2
4. Deduplicate Alignments using Picard MarkDuplicates
5. Call Macs2 Peaks using macs2

A pdf of the rulegraph is available here

Full details for each step are given below. Any additional ...

GRAVI: Gene Regulatory Analysis using Variable Inputs

This is a snakemake workflow for:

1. Performing sample QC
2. Calling ChIP peaks
3. Performing Differential Binding Analysis
4. Comparing results across ChIP targets

The minimum required input is one ChIP target with two conditions.

Full documentation can be found here

Snakemake Implementation

The basic workflow is written snakemake, requiring at least v7.7, and can be called using the following ...

This workflow take as input a collection of paired fastq. Remove adapters with cutadapt, map pairs with bowtie2 allowing dovetail. Keep MAPQ30 and concordant pairs. BAM to BED. MACS2 with "ATAC" parameters.

This workflow take as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will plot the number of reads for each fragment length.

ChIP-seq paired-end Workflow

Inputs dataset

• The workflow needs a single input which is a list of dataset pairs of fastqsanger.

Inputs values

• adapters sequences: this depends on the library preparation. If you don't know, use FastQC to determine if it is Truseq or Nextera.
• reference_genome: this field will be adapted to the genomes available for bowtie2.
• effective_genome_size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes).

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