.. _docs_gp_chipseq: .. spelling:word-list:: transposase Immunoprecipitation atacseq Transposon nucleosome atac ChIP Sequencing Pipeline ======================== :bdg-primary:`Version` |genpipes_version| .. include:: /common/new_gp_wizard.txt .. include:: /mouse_mm10_warning.inc .. tab-set:: .. tab-item:: Usage .. dropdown:: Command :open: .. code-block:: bash user@machine:~$ genpipes chipseq [options] [--genpipes_file GENPIPES_FILE.sh] user@machine:~$ bash GENPIPES_FILE.sh .. dropdown:: Options .. include:: opt_chipseq.inc .. include:: /common/gp_design_opt.inc .. include:: /common/gp_readset_opt.inc .. include:: /common/gp_common_opt.inc .. dropdown:: Example .. include:: /user_guide/pipelines/example_runs/chipseq.inc The commands will be sent to the job queue and you will be notified once each step is done. If everything runs smoothly, you should get `MUGQICexitStatus:0` or `Exit_status=0`. If that is not the case, then an error has occurred after which the pipeline usually aborts. To examine the errors, check the content of the job_output folder. .. include:: /user_guide/pipelines/notes/scriptfile_deprecation.inc .. card:: Test Dataset :link: docs_testdatasets :link-type: ref You can download the test dataset for this pipeline :ref:`here`. .. tab-item:: Schema :name: chipschema .. dropdown:: ChipSeq .. figure:: /img/pipelines/mmd/chipseq.mmd.png :align: center :alt: ChIP-Seq schema :figwidth: 95% :width: 100% Figure: Schema of ChIP Sequencing protocol .. figure:: /img/pipelines/mmd/legend.mmd.png :align: center :alt: dada2 ampseq :width: 100% :figwidth: 75% .. dropdown:: ATACSeq .. figure:: /img/pipelines/mmd/chipseq.atac.mmd.png :align: center :alt: ChIP-Seq schema atacseq option :figwidth: 95% :width: 100% Figure: Schema of ChIP Sequencing -t atacseq protocol .. figure:: /img/pipelines/mmd/legend.mmd.png :align: center :alt: dada2 ampseq :width: 100% :figwidth: 75% .. tab-item:: Steps .. dropdown:: ChIP-Seq .. list-table:: :widths: auto :class: table-responsive * - 1. - |picard_sam_to_fastq| * - 2. - |trimmomatic| * - 3. - |merge_trimmomatic_stats| * - 4. - |mapping_bwamem_sambamba| * - 5. - |sambamba_merge_bam| * - 6. - |sambamba_mark_dup| * - 7. - |sambamba_view_filter| * - 8. - |bedtools_black_filter| * - 9. - |metrics| * - 10. - |homer_make_tag_directory| * - 11. - |qc_metrics| * - 12. - |deeptools_qc| * - 13. - |homer_make_ucsc_file| * - 14. - |macs2_callpeak| * - 15. - |homer_annotate_peaks| * - 16. - |homer_find_motifs_genome| * - 17. - |annotation_graphs| * - 18. - |run_spp| * - 19. - |differential_binding| * - 20. - |ihec_metrics| * - 21. - |multiqc_report| * - 22. - |cram_output| * - 23. - |gatk_haplotype_caller| * - 24. - |merge_and_call_ind_gvcf| .. dropdown:: ATAC-Seq .. list-table:: :widths: auto :class: table-responsive * - 1. - |picard_sam_to_fastq| * - 2. - |trimmomatic| * - 3. - |merge_trimmomatic_stats| * - 4. - |mapping_bwamem_sambamba| * - 5. - |sambamba_merge_bam| * - 6. - |sambamba_mark_dup| * - 7. - |sambamba_view_filter| * - 8. - |bedtools_black_filter| * - 9. - |metrics| * - 10. - |homer_make_tag_directory| * - 11. - |qc_metrics| * - 12. - |homer_make_ucsc_file| * - 13. - |macs2_atacseq_callpeak| * - 14. - homer_annotate_peaks| * - 15. - |homer_find_motifs_genome| * - 16. - |annotation_graphs| * - 17. - |run_spp| * - 18. - |differential_binding| * - 19. - |ihec_metrics| * - 20. - |multiqc_report| * - 21. - |cram_output| * - 22. - |gatk_haplotype_caller| * - 23. - |merge_and_call_ind_gvcf| .. card:: .. include:: steps_chipseq.inc .. tab-item:: About .. card:: Chromatin Immunoprecipitation (ChIP) sequencing technique is used for mapping DNA-protein interactions. It is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. The ChIP-Seq workflow is based on the `ENCODE Project`_ workflow. The pipeline starts by trimming adapters and low quality bases and mapping the reads (single end or paired end ) to a reference genome using `Burrows-Wheeler Aligner`_ (BWA). Reads are filtered by mapping quality and duplicate reads are marked. It creates tag directories using `Homer routines`_. Peaks are called using `Model based Analysis for Chip Sequencing (MACS2)`_ and annotated using Homer. Binding motifs are also identified using Homer. Metrics are calculated based on `IHEC requirements`_. The ChIP-Seq pipeline can also be used for assay for transposase-accessible chromatin using sequencing `ATAC-Seq`_ samples. Use 'ATAC' protocol option to run the pipeline using ATAC-Seq. See :ref:`chipschema` tab for the pipeline workflow. Check the `README.md `_ file for implementation details. .. figure:: /img/pipelines/ChIP-Seq-hl-diag.png :align: center :alt: ChIP-Seq-HL Figure: Schematic representation of major methods used to detect functional elements in DNA (Source PLOS) **References** * `ChIP-Seq Guidelines`_ * `MUGQIC_Bioinfo_Chip-Seq.pptx`_ * `ChIP-Seq and Beyond `_ * `Schematic representation of major methods to detect functional elements in DNA `_ * `ChIP Sequencing and ATAC Sequencing `_ .. dropdown:: :material-outlined:`notifications;2em` Input requirements :color: info The Chip Sequencing protocol expects an input for the **Differential Binding** step. If pipeline users want to run this protocol without an input, they should skip the differential binding step and run it themselves locally. .. dropdown:: :material-outlined:`report;2em` Chip Sequencing Readset File :color: warning Please make sure you use the special :ref:`ChIPSeq Pipeline Readset file format` and not the general readset file format. .. _ref_chipseq_design_ff: .. dropdown:: :material-outlined:`settings;2em` Chip Sequencing Design File Format :color: muted .. include:: /user_guide/pipelines/design_fileformat/chipseq_design.inc .. The following are replacement texts used in this file .. |picard_sam_to_fastq| replace:: `Picard Sam to Fastq`_ .. |trimmomatic| replace:: `Trimmomatic`_ .. |merge_trimmomatic_stats| replace:: `Merge Trimmomatic Stats`_ .. |bedtools_black_filter| replace:: `Bedtools Blacklist Filter`_ .. |metrics| replace:: `Metrics`_ .. |homer_make_tag_directory| replace:: `Homer Make Tag Directory`_ .. |qc_metrics| replace:: `QC Metrics`_ .. |deeptools_qc| replace:: `Deeptools QC`_ .. |homer_make_ucsc_file| replace:: `Homer Make UCSC file`_ .. |macs2_callpeak| replace:: `MACS2 call peak`_ .. |macs2_atacseq_callpeak| replace:: `MACS2 ATAC-seq call peak`_ .. |homer_annotate_peaks| replace:: `Homer annotate peaks`_ .. |homer_find_motifs_genome| replace:: `Homer find motifs genome`_ .. |annotation_graphs| replace:: `Annotation Graphs`_ .. |run_spp| replace:: `Run SPP`_ .. |differential_binding| replace:: `Differential Binding`_ .. |ihec_metrics| replace:: `IHEC Metrics`_ .. |multiqc_report| replace:: `MultiQC Report`_ .. |mapping_bwamem_sambamba| replace:: `Mapping BWA Mem Sambamba`_ .. |sambamba_merge_bam| replace:: `SAMbamba Merge BAM`_ .. |sambamba_mark_dup| replace:: `SAMbamba Mark Duplicates`_ .. |sambamba_view_filter| replace:: `SAMbamba View Filter`_ .. |gatk_haplotype_caller| replace:: `GATK Haplotype Caller`_ .. |merge_and_call_ind_gvcf| replace:: `Merge and Call Individual GVCF`_ .. include:: repl_cram_op.inc .. The following are html link targets used in this text .. _ENCODE Project: https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements .. _Burrows-Wheeler Aligner: http://bio-bwa.sourceforge.net .. _Homer routines: http://homer.ucsd.edu/homer/ngs/ .. _Model based Analysis for Chip Sequencing (MACS2): https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137 .. _IHEC requirements: https://github.com/IHEC/ihec-assay-standards .. _ATAC-Seq: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/ .. _ChIP-Seq Guidelines: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/ .. _ChIP-Seq report: http://gqinnovationcenter.com/services/bioinformatics/tools/chipReport/index.html .. _ChIP-Seq Pipeline README: https://bitbucket.org/mugqic/genpipes/src/master/pipelines/chipseq/README.md .. _GenPipes ChIP-Seq pipeline implementation: https://bitbucket.org/mugqic/genpipes/src/master/pipelines/chipseq/ .. _ChIP-Seq Schema high resolution image: https://bitbucket.org/mugqic/genpipes/raw/master/resources/workflows/GenPipes_chipseq.png .. _MUGQIC_Bioinfo_ChIP-Seq.pptx: https://bitbucket.org/mugqic/genpipes/downloads/MUGQIC_Bioinfo_ChIP-Seq.pptx