التفاصيل البيبلوغرافية
| العنوان: |
ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference. |
| المؤلفون: |
Pranzatelli, Thomas J. F.1 thomas.pranzatelli@nih.gov, Michael, Drew G.1 drew.michael@nih.gov, Chiorini, John A.1 jchiorini@dir.nidcr.nih.gov |
| المصدر: |
BMC Genomics. 7/31/2018, Vol. 19 Issue 1, p1-13. 13p. 2 Diagrams, 5 Graphs. |
| مصطلحات موضوعية: |
*CHROMATIN, *ASSAYING apparatus, *GENOMES, *NUCLEOTIDE sequence, *NUCLEOTIDES |
| مستخلص: |
Background: Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution. Optimization of molecular protocols has enabled the molecular biologist to produce next-generation sequencing libraries in several hours, leaving the analysis of sequencing data as the primary obstacle to wide-scale deployment of accessibility profiling assays. To address this obstacle we have developed an optimized and efficient pipeline for the analysis of ATAC-seq and DNase1-seq data. Results: We executed a multi-dimensional grid-search on the NIH Biowulf supercomputing cluster to assess the impact of parameter selection on biological reproducibility and ChIP-seq recovery by analyzing 4560 pipeline configurations. Our analysis improved ChIP-seq recovery by 15% for ATAC-seq and 3% for DNase1-seq and determined that PCR duplicate removal improves biological reproducibility by 36% without significant costs in footprinting transcription factors. Our analyses of down sampled reads identified a point of diminishing returns for increased library sequencing depth, with 95% of the ChIP-seq data of a 200 million read footprinting library recovered by 160 million reads. Conclusions: We present optimized ATAC-seq and DNase-seq pipelines in both Snakemake and bash formats as well as optimal sequencing depths for ATAC-seq and DNase-seq projects. The optimized ATAC-seq and DNase1-seq analysis pipelines, parameters, and ground-truth ChIP-seq datasets have been made available for deployment and future algorithmic profiling. [ABSTRACT FROM AUTHOR] |
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