{"lab": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Input paired-end reads are merged according to orientation and trimmed with ``Trimmomatic`` version 0.36. In particular, Trimmomatic is called in paired-end mode (PE) with added parameters applied in the order they are specified: ::\n\n ILLUMINACLIP:/TruSeq3-PE.fa:2:15:4:1:true MINLEN:20\n\n* ``ILLUMINACLIP`` trims adapter sequences specified by ``TruSeq3-PE.fa``\n\n * ``2`` (seedMismatches) is a maximum mismatch count for full matches.\n * ``15`` (palindromeClipThreshold) indicates the quality of match required for palindrome read alignment. The palindrome mode identifies adapter read-through by comparing the forward and reverse reads.\n * ``4`` (simpleClipThreshold) indicates the accuracy a match between an adapter and read must have.\n * ``1`` (minAdapterLength) indicates minimum adapter length for palindrome mode. This value is minimized to optimize adapter detection, leveraging a low false positive rate for palindrome mode.\n * ``true`` (keepBothReads) indicates that both reads should be kept when an adapter is trimmed in palindrome mode.\n* ``MINLEN:20`` removes reads which are less than 20 bases (performed after all other trimming is completed).\n\nTo learn more about these settings, refer to the `Trimmomatic documentation `_.\n", "name": "resources.data-analysis.cut-and-run-pipeline.trim", "award": {"project": "4DN", "name": "2U01CA200059-06", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "status": "current", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "center_title": "DCIC - Park", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Trimming", "status": "released", "aliases": ["4dn-dcic-lab:resources.data-analysis.cut-and-run-pipeline.trim"], "options": {"filetype": "rst", "collapsible": false, "default_open": true, "convert_ext_links": true}, "date_created": "2021-10-05T20:04:35.594913+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-08-19T23:17:44.209019+00:00"}, "schema_version": "2", "@id": "/static-sections/7cc17eae-421e-468d-972d-952f204fd532/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "7cc17eae-421e-468d-972d-952f204fd532", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.545f1931-792c-4a7e-83b3-3e91baea4e30"]}, "display_title": "Trimming", "external_references": [], "content": "Input paired-end reads are merged according to orientation and trimmed with ``Trimmomatic`` version 0.36. In particular, Trimmomatic is called in paired-end mode (PE) with added parameters applied in the order they are specified: ::\n\n ILLUMINACLIP:/TruSeq3-PE.fa:2:15:4:1:true MINLEN:20\n\n* ``ILLUMINACLIP`` trims adapter sequences specified by ``TruSeq3-PE.fa``\n\n * ``2`` (seedMismatches) is a maximum mismatch count for full matches.\n * ``15`` (palindromeClipThreshold) indicates the quality of match required for palindrome read alignment. The palindrome mode identifies adapter read-through by comparing the forward and reverse reads.\n * ``4`` (simpleClipThreshold) indicates the accuracy a match between an adapter and read must have.\n * ``1`` (minAdapterLength) indicates minimum adapter length for palindrome mode. This value is minimized to optimize adapter detection, leveraging a low false positive rate for palindrome mode.\n * ``true`` (keepBothReads) indicates that both reads should be kept when an adapter is trimmed in palindrome mode.\n* ``MINLEN:20`` removes reads which are less than 20 bases (performed after all other trimming is completed).\n\nTo learn more about these settings, refer to the `Trimmomatic documentation `_.\n", "filetype": "rst", "content_as_html": "

Input paired-end reads are merged according to orientation and trimmed with Trimmomatic version 0.36. In particular, Trimmomatic is called in paired-end mode (PE) with added parameters applied in the order they are specified:

\nILLUMINACLIP:<path>/TruSeq3-PE.fa:2:15:4:1:true MINLEN:20\n
  • ILLUMINACLIP trims adapter sequences specified by TruSeq3-PE.fa
    • 2 (seedMismatches) is a maximum mismatch count for full matches.
    • 15 (palindromeClipThreshold) indicates the quality of match required for palindrome read alignment. The palindrome mode identifies adapter read-through by comparing the forward and reverse reads.
    • 4 (simpleClipThreshold) indicates the accuracy a match between an adapter and read must have.
    • 1 (minAdapterLength) indicates minimum adapter length for palindrome mode. This value is minimized to optimize adapter detection, leveraging a low false positive rate for palindrome mode.
    • true (keepBothReads) indicates that both reads should be kept when an adapter is trimmed in palindrome mode.
  • MINLEN:20 removes reads which are less than 20 bases (performed after all other trimming is completed).

To learn more about these settings, refer to the Trimmomatic documentation.

", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}