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SEAseq

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Single-End Antibody SEQuencing pipeline (abbreviated as SEAseq) is a comprehensive automated pipeline for ChIP-Seq/CUT&RUN data analysis. Speaking broadly, it containerizes and joins field-standard, open-source tools for processing raw data and performing a wide array of basic analyses.

SEAseq analyses include alignment, peak calling, motif analysis, read coverage profiling, clustered peak (e.g. super-enhancer) identification, and quality assessment metrics, as well as automatic interfacing with data in GEO/SRA. The easy-to-use and flexibility of SEAseq makes it a reliable and efficient resource for ensuring high quality ChIP-Seq analysis, especially in research environments lacking computational infrastructure or expertise.

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What's new in Version 3.0

  • PEAseq pipeline.

    PEAseq (Paired-End Antibody Sequencing Pipeline) performs all analysis provided in SEAseq and also in a paired-end aware manner; results from SEAseq will be stored under /single-end_mode.

  • A new color-rank scheme for the Quality Metrics and Evaluation Report HTML.

SEAseq on Linux or HPC

SEAseq pipeline requires the Cromwell jar runner, Docker or Singularity, Java (v1.8.0) and about 30GB of supplemental data.

View /test folder for example usage.

NOTE : HPC platforms using Singularity will require a configuration file to properly execute cromwell. Please consult hpc-configurations for more details.

St. Jude Users please consult SEAseq on St. Jude HPC

SEAseq on St. Jude cloud

Before you can run SEAseq on St. Jude Cloud, you must first create a workspace in DNAnexus for the run. Refer to the general workflow guide to learn how to create a DNAnexus workspace for each workflow run.

You can navigate to the SEAseq workflow page here.

Citation

Adetunji, M.O., Abraham, B.J. SEAseq: a portable and cloud-based chromatin occupancy analysis suite. BMC Bioinformatics 23, 77 (2022). https://doi.org/10.1186/s12859-022-04588-z