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RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.
3' mRNA-seq methods are generally cheaper per sample than standard bulk RNA-seq methods. [2] [7] [8] [9] This is because of the lower sequencing depth required due to only the 3' end of mRNA molecules being sequenced instead of the whole length of entire transcripts. Read depths of between one million and five million reads are recommended in ...
Unlike standard bulk RNA-seq methods which require around 30 million reads per sample for robust gene expression information, for BRB-seq, a sequencing depth of between one and five million reads per sample is sufficient to detect the majority of expressed genes in a sample. Lowly expressed genes can be detected by sequencing at higher depths.
Rcount Rcount: simple and flexible RNA-Seq read counting. rDiff is a tool that can detect differential RNA processing (e.g. alternative splicing, polyadenylation or ribosome occupancy). RNASeqPower Calculating samples Size estimates for RNA Seq studies. R package version.
RNA-Seq operations are highly repetitious and benefit from parallelised computation but modern algorithms mean consumer computing hardware is sufficient for simple transcriptomics experiments that do not require de novo assembly of reads. [98] A human transcriptome could be accurately captured using RNA-Seq with 30 million 100 bp sequences per ...
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]
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