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REEP5 is expressed across a number of tissues at a relatively high level, with at least 20 Reads Per Kilobase of transcript, per Million mapped reads appearing in adrenal, fat, gall bladder, heart, kidney, prostate, lung, and urinary bladder tissues. [14] Expression is even more highly elevated in brain and thyroid tissues. [14]
Therefore, the total number of reads generated in a single experiment is typically normalized by converting counts to fragments, reads, or counts per million mapped reads (FPM, RPM, or CPM). The difference between RPM and FPM was historically derived during the evolution from single-end sequencing of fragments to paired-end sequencing.
Sequence coverage (or depth) is the number of unique reads that include a given nucleotide in the reconstructed sequence. [1] [2] Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. [3] Physical coverage, the cumulative length of reads or read pairs expressed as a multiple of ...
The minimal genome corresponds to small genome sizes, as bacterial genome size correlates with the number of protein-coding genes, typically one gene per kilobase. [1] Mycoplasma genitalium, with a 580 kb genome and 482 protein-coding genes, is a key model for minimal genomes. [9]
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]
It is already adapted to align long reads (third-generation sequencing technologies) and can reach speeds of 45 million paired reads per hour per processor. [49] Subjunc [44] is a specialized version of Subread. It uses all mappable regions in an RNA-seq read to discover exons and exon-exon junctions.
In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in terms of a million base pairs, or megabase (Mb). The human genome has a gene density of 11-15 genes/Mb, while the genome of the C. elegans roundworm is estimated to have 200.
While single-read accuracy is 87%, consensus accuracy has been demonstrated at 99.999% with multi-kilobase read lengths. [ 37 ] [ 38 ] In 2015, Pacific Biosciences released a new sequencing instrument called the Sequel System, which increases capacity approximately 6.5-fold.