Workflows for genomics topic with tag ENCODE
ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline This ChIP-Seq pipeline is based off the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline specifications (by Anshul Kundaje) in this [google doc](https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit#).
This is the ENCODE-DCC RNA-sequencing pipeline. The scope of the pipeline is to align reads, generate signal tracks, and quantify genes and isoforms. RNA-seq data is valuable as it allows the measure of RNA expression levels as a transcriptional readout and the study of RNA structures in order to understand how RNA-based mechanisms impact gene regulation and thus disease and phenotypic variation. Since RNA populations are diverse, the ENCODE Consortium has developed the following RNA-seq pipelines:
This is the ENCODE-DCC Long read RNA-seq pipeline. This pipeline can handle data from both PacBio and Oxford Nanopore platforms. Pipeline does read alignment, corrects for mismatches, microindels and non-canonical splice junctions and then provides quantitations and QC-metrics.
This is the ENCODE-DCC Micro RNA-sequencing pipeline. The scope of the pipeline is to cut adapters, align reads, generate signal tracks, and quantify genes. MicroRNA-seq allows researchers to characterize and quantify the expression and prevalence of the small non-coding RNA moleccules known as microRNA. These molecules may play an important role in diseases, and significant effort is underway to understand their effects across a variety of tissue types and cells. For effective processing, the average insert size must be no more than 30 bases.