Explore Workflows

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/qc_wgs_mouse.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf5.cwl

Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: 8c4e7372247a7f4ed9ed478ef8ea1d239bc88af0

SoupX Estimate ==============

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

Path: workflows/soupx.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3

Interval overlapping alignments counts ====================================== Reports the count of alignments from multiple samples that overlap specific intervals.

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

Path: workflows/bedtools-multicov.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3

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: 30031ca5e69cec603c4733681de54dc7bffa20a3

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/extract_capture_kit_http.cwl

Branch/Commit ID: 6b43e8b03256492f2b36ffcf548704daaafee6f6

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/pvacseq.cwl

Branch/Commit ID: 040a3d1a719736d7fce6db83702d3fb7f9d69eac