QuestionsCategory: ChIP-Seq Data AnalysisPipelines and QC: Which ChIP-seq pipelines mentioned in your talk can handle paired-end reads?
stonelakeak@nih.gov Staff asked 5 months ago

Which ChIP-seq pipelines mentioned in your talk can handle paired-end reads?

1 Answers
stonelakeak@nih.gov Staff answered 5 months ago

The CCBR Pipeliner running on Biowulf can handle both, single and pair-end, datasets seamlessly. The DNAnexus version only supports single-end data at the moment. Having said that, one can always only use “Read1” of the any paired-end dataset and run it as “pseudo” single end dataset on DNAnexus. If all QC metrics are generally met, then we do not expect much difference in results from running your data in this “pseudo” single end mode when compared to the paired-end execution. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.