4 items tagged with 'ChIP'.
This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.
Created: 5th Sep 2023 at 03:01
Views: 45, Downloads: 11
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.
Created: 21st Oct 2022 at 03:01, Last updated: 1st Sep 2023 at 03:01
Views: 662, Downloads: 29
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.
Created: 21st Oct 2022 at 03:01, Last updated: 1st Sep 2023 at 03:01
Views: 675, Downloads: 25
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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Created: 15th Oct 2022 at 03:01
Views: 431, Downloads: 7