What does DNase-seq measure?

DNase-seq (DNase I hypersensitive sites sequencing) is a method in molecular biology used to identify the location of regulatory regions, based on the genome-wide sequencing of regions sensitive to cleavage by DNase I.

What is paired end read?

The term ‘paired ends’ refers to the two ends of the same DNA molecule. So you can sequence one end, then turn it around and sequence the other end. The two sequences you get are ‘paired end reads’.

What is the difference between single end and paired end reads?

Single-end vs. In single-end reading, the sequencer reads a fragment from only one end to the other, generating the sequence of base pairs. In paired-end reading it starts at one read, finishes this direction at the specified read length, and then starts another round of reading from the opposite end of the fragment.

What is the purpose of paired end reads?

Paired-end DNA sequencing reads provide high-quality alignment across DNA regions containing repetitive sequences, and produce long contigs for de novo sequencing by filling gaps in the consensus sequence. Paired-end DNA sequencing also detects common DNA rearrangements such as insertions, deletions, and inversions.

What are paired end reads in DNA sequencing?

Many sequencing library preparation kits include an option to generate so-called “ paired-end reads “. In “short-read” sequencing, intact genomic DNA is sheared into several million short DNA fragments called “reads”.

When to use a single end RNA Seq?

Standard mRNA- or total RNA-seq: Single-end 50 or 75bp reads are mostly used for general gene expression profiling. To study alternative splicing variants, paired-end, longer reads (up to 150 bp) are often requested.

How does DNase seq adapt to modern DNA sequencing?

DNase-seq adapts traditional DNase I footprinting 1 and leverages modern DNA sequencing to identify regions of the genome where regulatory factors interact with DNA to modify chromatin structure and gene transcription 1, 2, 3, 4, 5.

Which is the pipeline for encode DNase seq?

This is the uniform processing pipeline for ENCODE DNase-seq experiments. It uses WDL and Caper (a wrapper over Cromwell) to specify and run the processing steps, and Docker to ensure a reproducible and portable compute environment.