Explore Workflows

https://github.com/ncbi/pgap.git

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 686b570a9fa46f3ace3f8e9935490b75df86a1fc

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/mut.cwl

Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/marianas/collapsed_fastq_to_bam.cwl

Branch/Commit ID: f8b57834ad0ce78e4d5bdd90ed0991923685d87f

https://github.com/arvados/bh20-seq-resource.git

Path: workflows/pangenome-generate/pangenome-generate.cwl

Branch/Commit ID: 30f3f8b0e9efbc954518fc8ea621b53c9591c83a

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/indexing_bed.cwl

Branch/Commit ID: 70eec658fd1b92c4d0e3b24146820010b5983d41

Cross-Linking ImmunoPrecipitation ================================= `CLIP` (`cross-linking immunoprecipitation`) is a method used in molecular biology that combines UV cross-linking with immunoprecipitation in order to analyse protein interactions with RNA or to precisely locate RNA modifications (e.g. m6A). (Uhl|Houwaart|Corrado|Wright|Backofen|2017)(Ule|Jensen|Ruggiu|Mele|2003)(Sugimoto|König|Hussain|Zupan|2012)(Zhang|Darnell|2011) (Ke| Alemu| Mertens| Gantman|2015) CLIP-based techniques can be used to map RNA binding protein binding sites or RNA modification sites (Ke| Alemu| Mertens| Gantman|2015)(Ke| Pandya-Jones| Saito| Fak|2017) of interest on a genome-wide scale, thereby increasing the understanding of post-transcriptional regulatory networks. The identification of sites where RNA-binding proteins (RNABPs) interact with target RNAs opens the door to understanding the vast complexity of RNA regulation. UV cross-linking and immunoprecipitation (CLIP) is a transformative technology in which RNAs purified from _in vivo_ cross-linked RNA-protein complexes are sequenced to reveal footprints of RNABP:RNA contacts. CLIP combined with high-throughput sequencing (HITS-CLIP) is a generalizable strategy to produce transcriptome-wide maps of RNA binding with higher accuracy and resolution than standard RNA immunoprecipitation (RIP) profiling or purely computational approaches. The application of CLIP to Argonaute proteins has expanded the utility of this approach to mapping binding sites for microRNAs and other small regulatory RNAs. Finally, recent advances in data analysis take advantage of cross-link–induced mutation sites (CIMS) to refine RNA-binding maps to single-nucleotide resolution. Once IP conditions are established, HITS-CLIP takes ~8 d to prepare RNA for sequencing. Established pipelines for data analysis, including those for CIMS, take 3–4 d. Workflow -------- CLIP begins with the in-vivo cross-linking of RNA-protein complexes using ultraviolet light (UV). Upon UV exposure, covalent bonds are formed between proteins and nucleic acids that are in close proximity. (Darnell|2012) The cross-linked cells are then lysed, and the protein of interest is isolated via immunoprecipitation. In order to allow for sequence specific priming of reverse transcription, RNA adapters are ligated to the 3' ends, while radiolabeled phosphates are transferred to the 5' ends of the RNA fragments. The RNA-protein complexes are then separated from free RNA using gel electrophoresis and membrane transfer. Proteinase K digestion is then performed in order to remove protein from the RNA-protein complexes. This step leaves a peptide at the cross-link site, allowing for the identification of the cross-linked nucleotide. (König| McGlincy| Ule|2012) After ligating RNA linkers to the RNA 5' ends, cDNA is synthesized via RT-PCR. High-throughput sequencing is then used to generate reads containing distinct barcodes that identify the last cDNA nucleotide. Interaction sites can be identified by mapping the reads back to the transcriptome.

https://github.com/datirium/workflows.git

Path: workflows/clipseq-se.cwl

Branch/Commit ID: d1bef74924efcb8bfaa00987b3f148d5a192b7a9

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: e59538cd9899a88d7e31e0f259bc56734f604383

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/conpair/0.2/conpair-master.cwl

Branch/Commit ID: 08e592a521057cef4982c1d4111d2e3b30ea3f2f

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/readgroups_bam_to_readgroups_fastq_lists.cwl

Branch/Commit ID: 20a901f44c9fb0e6f4ee3c40ec33fa4b1c8ef005