What is encode RNA-seq?
ENCODE RNA-seq pipeline 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.
What is long RNA-seq?
Long read RNA-seq can sequence individual transcript molecules in full, making it possible to see exactly which splice junctions were present in context. Long read RNA-seq can be used to characterize isoforms on a transcriptome-wide scale, and also to perform quantification on the gene and isoform level.
What is encode pipeline?
The ENCODE Data Coordinating Center Uniform Processing Pipelines are designed to create high-quality, consistent, and reproducible data. Pipelines are composed of discrete steps that can represent an algorithm, a software tool, or a file format manipulation. To learn more, select a specific pipeline.
What is RNA-seq pipeline?
RNA sequencing (RNA-seq) is a high throughput technology that provides unique insights into the transcriptome. It has a wide variety of applications in quantifying genes/isoforms, detecting non-coding RNA, alternative splicing, and splice junctions. Several RNA-seq analysis pipelines are proposed to date.
How does bulk RNA-Seq work?
Bulk RNA-Seq experiments provide a view of gene expression of an entire sample. This is done by dissociating the sample into individual single cells, identifying the cell types, and measuring the expression products of each cell.
What is the difference between RNA-Seq and microarray?
The main difference between RNA-Seq and microarrays is that the former allows for full sequencing of the whole transcriptome while the latter only profiles predefined transcripts/genes through hybridization.
What does ATAC-seq measure?
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. ATAC-seq is a faster and more sensitive analysis of the epigenome than DNase-seq or MNase-seq.
What is scATAC seq?
Abstract. Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells.
What are the main steps in typical RNA-Seq data analysis pipeline?
For most RNA‐seq studies, the data analyses consist of the following key steps [5, 6]: (1) quality check and preprocessing of raw sequence reads, (2) mapping reads to a reference genome or transcriptome, (3) counting reads mapped to individual genes or transcripts, (4) identification of differential expression (DE) …
How many cells are required for bulk RNA-Seq?
We only need 100 cells for bulk RNA sequencing.
When do you use encode for RNA Seq?
The ENCODE RNA-seq pipeline for small RNAs can be used for libraries generated from rRNA-depleted total RNA that are size-selected to be shorter than approximately 200 nucleotides. Data may be paired-ended and stranded or single-ended and unstranded.
How many replicates are needed for small RNA Seq?
An small RNA-seq experiment is an RNA-seq assay in which the average library insert size is <200 base pairs. Experiments should have two or more replicates. Assays performed using EN-TEx samples may be exempted due to limited availability of experimental material.
Where can I find the RNA Seq pipeline?
The small RNA-seq pipeline was developed as a part of the ENCODE Uniform Processing Pipelines series. The full pipeline code is freely available on Github and can be run on DNAnexus (link requires account creation) at their current pricing.
What are the alignment files for bulk RNA Seq?
Alignment files are mapped to the GRCh38, hg19, or mm10 sequences. Gene and transcript quantification files are annotated to GENCODE V24, V19, or M4. Experimental guidelines for bulk RNA-seq experiments can be found here.