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However, using such a low input of cells may be associated with low library complexity which results in a high percentage of duplicate reads during library preparation. [4] Standard Hi-C gives data on pairwise interactions at the resolution of 1 to 10 Mb, requires high sequencing depth and the protocol takes around 7 days to complete. [3] [4] [14]
qRNASeq script The qRNAseq tool can be used to accurately eliminate PCR duplicates from RNA-Seq data if Molecular Indexes™ or other stochastic labels have been used during library prep. SHERA [42] a SHortread Error-Reducing Aligner. XORRO Rapid Paired-End Read Overlapper. DecontaMiner [43] detects contamination in RNA-Seq data.
In 2009, Roche launched the GS Junior, a bench top version of the 454 sequencer with read length up to 400bp, and simplified library preparation and data processing. One of the advantages of 454 systems is their running speed. Manpower can be reduced with automation of library preparation and semi-automation of emulsion PCR.
Data generation artifacts (also known as technical variance): The reagents (e.g., library preparation kit), personnel involved, and type of sequencer (e.g., Illumina, Pacific Biosciences) can result in technical artifacts that might be mis-interpreted as meaningful results. As with any scientific experiment, it is prudent to conduct RNA-Seq in ...
The DNA sequencing is done on a chip that contains many ZMWs. Inside each ZMW, a single active DNA polymerase with a single molecule of single stranded DNA template is immobilized to the bottom through which light can penetrate and create a visualization chamber that allows monitoring of the activity of the DNA polymerase at a single molecule level.
The company's first scientific instrument, called the PacBio RS, was released to a limited set of customers in late 2010., with full commercial release in early 2011. [17] [8] Sequencing provider GATC Biotech was selected by Pacific Biosciences as its first European service provider in late 2010. [18]