NGI during Covid-19 outbreak

NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.

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ChIP-seq analysis

Runs with ChIP sequencing data. Pre-processes raw data from FastQ inputs, aligns the reads and performs peak calling and extensive quality-control on the results.

ChIP-Seq is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-seq) data analysis. The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs peak calling and extensive quality-control on the results.

nf-core/chipseq

https://github.com/nf-core/chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline. - https://nf-co.re/chipseq

When we run analysis

We run this analysis routinely for all ChIP-seq projects where we have prepared the sequencing library in-house. If you have prepared a library yourself and we are just sequencing, please get in touch and mention that you would like us to run this analysis.

The analysis works with any of the species that have a reference genome available in AWS-iGenomes. If in doubt, please ask whether we can run the pipeline for you.

Input data

bcl2fastq demultiplexed FastQ files and a genome reference.

Results

The pipeline generates aligned BAM-files, files with information about called peaks, along with numerous quality control metrics. For more information, please see https://nf-co.re/chipseq/docs/output.

Applications
Method Status

Service

We are routinely running this method. Please visit the Order Portal to place an order.

Keywords
Compatible Methods