UMI is an acronym for Unique Molecular Identifier.  UMIs are complex indices added to sequencing libraries before any PCR amplification steps, enabling the accurate bioinformatic identification of PCR duplicates. UMIs are also known as “Molecular Barcodes” or “Random Barcodes”.  The…

Illumina has posted a Beginners Guide on their technology at: https://www.illumina.com/science/technology/next-generation-sequencing/beginners.html Please also see our information at: https://dnatech.genomecenter.ucdavis.edu/illumina-high-throughput-sequencing/

Depending on sequencer and in case of the HiSeq 4000 even depending on run type (single-end or paired-end) Illumina uses different approaches to sequence the indices.   Please find detailed information here: indexed-sequencing-overview-guide-15057455-04-Illumina-pages1to8 The correct orientation of the barcode sequence fuehrer depends…

It is generally recommended to sequence 50 million or more reads/library-molecules  per ATAC-seq sample for open chromatin detection and differential analysis (Buenrostro et al. 2015) and 200 million reads for TF footprinting (Yan et al. 2020).  Preferred are paired-end sequencing…

The Illumina specifications are based on the Illumina PhiX control library. Better or similar yields can be expected for other high complexity libraries (e.g. genomic, RNA-seq libraries) if they are within the recommended insert size ranges and do not average extreme GC-contents.…

All sequencing data will be available for secure download via our SLIMS server. Illumina sequencing data will be delivered as compressed FASTQ files. By default the data will be de-multiplexed (e.g. split according to sample).  Each SLIMS directory will further…