A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages
Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Se...
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| Format: | Article |
| Language: | English |
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BioMed Central
2017-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-15-11.pdf |
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| author | Seung-Jin Park Jong-Hwan Kim Byung-Ha Yoon Seon-Young Kim |
| author_facet | Seung-Jin Park Jong-Hwan Kim Byung-Ha Yoon Seon-Young Kim |
| author_sort | Seung-Jin Park |
| collection | DOAJ |
| description | Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. ‘dada2’ performs trimming of the high-throughput sequencing data. ‘QuasR’ and ‘mosaics’ perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, ‘ChIPseeker’ performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git. |
| format | Article |
| id | doaj-art-9a492c4306dd4d098bf4ebcf6c58e9e2 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2017-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-9a492c4306dd4d098bf4ebcf6c58e9e22025-02-02T15:51:56ZengBioMed CentralGenomics & Informatics1598-866X2234-07422017-03-01151111810.5808/GI.2017.15.1.11201A ChIP-Seq Data Analysis Pipeline Based on Bioconductor PackagesSeung-Jin Park0Jong-Hwan Kim1Byung-Ha Yoon2Seon-Young Kim3Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. ‘dada2’ performs trimming of the high-throughput sequencing data. ‘QuasR’ and ‘mosaics’ perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, ‘ChIPseeker’ performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.http://genominfo.org/upload/pdf/gni-15-11.pdfchromatin immunoprecipitationdata analysisnext-generation sequencingstatistical |
| spellingShingle | Seung-Jin Park Jong-Hwan Kim Byung-Ha Yoon Seon-Young Kim A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages Genomics & Informatics chromatin immunoprecipitation data analysis next-generation sequencing statistical |
| title | A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages |
| title_full | A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages |
| title_fullStr | A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages |
| title_full_unstemmed | A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages |
| title_short | A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages |
| title_sort | chip seq data analysis pipeline based on bioconductor packages |
| topic | chromatin immunoprecipitation data analysis next-generation sequencing statistical |
| url | http://genominfo.org/upload/pdf/gni-15-11.pdf |
| work_keys_str_mv | AT seungjinpark achipseqdataanalysispipelinebasedonbioconductorpackages AT jonghwankim achipseqdataanalysispipelinebasedonbioconductorpackages AT byunghayoon achipseqdataanalysispipelinebasedonbioconductorpackages AT seonyoungkim achipseqdataanalysispipelinebasedonbioconductorpackages AT seungjinpark chipseqdataanalysispipelinebasedonbioconductorpackages AT jonghwankim chipseqdataanalysispipelinebasedonbioconductorpackages AT byunghayoon chipseqdataanalysispipelinebasedonbioconductorpackages AT seonyoungkim chipseqdataanalysispipelinebasedonbioconductorpackages |