AUTHOR=Carroll Thomas S. , Liang Ziwei , Salama Rafik , Stark Rory , de Santiago Ines 

TITLE=Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

JOURNAL=Frontiers in Genetics

VOLUME=Volume 5 - 2014

YEAR=2014

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2014.00075

DOI=10.3389/fgene.2014.00075

ISSN=1664-8021

ABSTRACT=With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium’s large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. <br/>In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied.  Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency. <br/>