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Gene length: Longer genes will have more fragments/reads/counts than shorter genes if transcript expression is the same. This is adjusted by dividing the FPM by the length of a feature (which can be a gene, transcript, or exon), resulting in the metric fragments per kilobase of feature per million mapped reads (FPKM). [90]
Sequencing technologies vary in the length of reads produced. Reads of length 20-40 base pairs (bp) are referred to as ultra-short. [2] Typical sequencers produce read lengths in the range of 100-500 bp. [3] However, Pacific Biosciences platforms produce read lengths of approximately 1500 bp. [4] Read length is a factor which can affect the results of biological studies. [5]
There are two common methods in which to construct a DNA molecular-weight size marker. [3] One such method employs the technique of partial ligation. [3] DNA ligation is the process by which linear DNA pieces are connected to each other via covalent bonds; more specifically, these bonds are phosphodiester bonds. [4]
Max Gb per Run Roche 454 Clonal-emPCR Pyrosequencing 400‡ 0.42 0.40-0.60 GS FLX Titanium Clonal-emPCR Pyrosequencing 400‡ 0.42 0.035 Illumina MiSeq Clonal Bridge Amplification Reversible Dye Terminator 2x300 0.17-2.7 15 Illumina HiSeq Clonal Bridge Amplification Reversible Dye Terminator 2x150 0.3-11 [12] 1000 [13] Illumina Genome Analyzer IIX
In 2012, with cameras operating at more than 10 MHz A/D conversion rates and available optics, fluidics and enzymatics, throughput can be multiples of 1 million nucleotides/second, corresponding roughly to 1 human genome equivalent at 1x coverage per hour per instrument, and 1 human genome re-sequenced (at approx. 30x) per day per instrument ...
Genome size ranges (in base pairs) of various life forms. Genome size is the total amount of DNA contained within one copy of a single complete genome.It is typically measured in terms of mass in picograms (trillionths or 10 −12 of a gram, abbreviated pg) or less frequently in daltons, or as the total number of nucleotide base pairs, usually in megabases (millions of base pairs, abbreviated ...
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The level of unique gene expression is represented by the count of transcripts present per million molecules, similar to SAGE output. A significant advantage is the larger library size compared with SAGE. An MPSS library typically holds 1 million signature tags, which is roughly 20 times the size of a SAGE library.