Epigenetic reprogramming towards mesenchymal-epithelial transition in ovarian cancer-associated mesenchymal stem cells drives metastasis

Fan, Huihui; Atiya, Huda I.; Wang, Yeh; Pisanic, Thomas R.; Wang, Jeff; Shih, Ie‐Ming; Foy, Kelly K.; Frisbie, Leonard; Chandler, Chelsea; Shen, Hui; Coffman, Lan

doi:10.1101/2020.02.25.964197

Cited by 1 publication

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“…PEPATAC does not rely on any specific local or cloud computing infrastructure, and it has already been deployed successfully in various compute environments at multiple research institutes to yield several peer-reviewed studies 10–14 . To simplify installation, we also enable a computing environment with the command-line tools required to run PEPATAC using either docker or singularity with the bulker multi-container environment manager 15 .…”

Section: Introductionmentioning

confidence: 99%

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PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

Smith

Corces

et al. 2020

Preprint

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Motivation: As chromatin accessibility data from ATAC-seq experiments continues to expand, there is continuing need for standardized analysis pipelines. Here, we present PEPATAC, an ATAC-seq pipeline that is easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. Results: PEPATAC leverages unique features of ATAC-seq data to optimize for speed and accuracy, and it provides several unique analytical approaches. Output includes convenient quality control plots, summary statistics, and a variety of generally useful data formats to set the groundwork for subsequent project-specific data analysis. Downstream analysis is simplified by a standard definition format, modularity of components, and metadata APIs in R and Python. It is restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also demonstrate the advantage of aligning to the mitochondrial genome serially, which improves the accuracy of alignment statistics and quality control metrics. PEPATAC is a robust and portable first step for any ATAC-seq project. Availability: BSD2-licensed code and documentation at https://pepatac.databio.org.

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Section: Introductionmentioning

confidence: 99%

“…PEPATAC does not rely on any specific local or cloud computing infrastructure, and it has already been deployed successfully in various compute environments at multiple research institutes to yield numerous peerreviewed studies (10)(11)(12)(13)(14). While all ATAC-seq pipelines use several common bioinformatic tools (Fig.…”

Section: Introductionmentioning

confidence: 99%

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

Smith

Corces

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

Epigenetic reprogramming towards mesenchymal-epithelial transition in ovarian cancer-associated mesenchymal stem cells drives metastasis

Cited by 1 publication

References 57 publications

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

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