ChIP-seq Data quality and Analysis Pipeline


  • ChIP-seq experiment has been a mature and wide-spread technique for detecting the transcription factor, histone modification and chromatin regulator distribution on the genome scale. DNase-seq is a high-throughput technoque for finding the markers of open chromatin regions.
  • Along with the popularity of the technique and the increasingly huge number of highthroughput datasets, it may be confusing for biologists to get a quick and easy access to understand their biological meaning, and the same important thing is the unbiased judgement of the data quality. So, it’s necessary for us to establish a universal and user-friendly ChIP-seq data analysis pipeline for biologists.
  • For bioinformaticians, this may be one of the most extensible and flexible ChIP-seq and DNase-seq pipeline implemented with python so far.
  • ChiLin has been used in many Cistrome related projects which generated thousands of ChIP-seq and DNase-seq datasets.


ChiLin provides a more flexible solution for understanding the ChIP-seq analysis workflow. ChiLin is intimately part of the Cistrome project. ChiLin has been fully tested on Ubuntu, CentOS, and Mac, and validate nearly 9000 datasets on centos 6.0 with slurm system, the metrics will be released after the publish of ChiLin paper. Cistrome related quality metrics will be released along with the paper.