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Transcriptome sequencing technology, mRNA-seq, is a transcriptome research method based on second-generation sequencing technology. RNA sequencing is a technology that uses the ability of Next Generation Sequencing(NGS) to reveal a snapshot of the presence and quantity of RNA from a genome at the given moment. Compared with genomic sequencing, the transcriptome is a dynamic process that is constantly changing. With the development of sequencing technology, the coverage of measurable DNA bases has increased and the throughput of sample output has increased. It helps to sequence RNA transcripts in cells, and provides details including alternative splicing transcription, post-transcriptional modification, gene fusion, mutations/SNPs, and changes in gene expression.
This pipeline is released by the BMAP team.
To enable researchers to further evaluate the accuracy of the RNA-seq analysis pipeline, a set of RNA-seq standard data which included transcriptome sequencing data and qPCR data for approximately 959 genes across 8 samples was constructed based on the SEQC database[1]
The accuracy of RNA-seq pipeline was assessed by comparing the analysis results of the standard data with the relative gene expression values obtained by qPCR. Due to the non-normal distribution of gene expression data, the Spearman correlation coefficient was employed to measure the accuracy of the analysis process. The RNA-seq pipeline achieved a mean score of spearman score with 0.8446, and the accuracy rate was determined to be 85.3%
The standardized analysis pipeline for transcriptomic data was established in BMAP following the best guidelines in a benchmark analysis study[2]
[1]Consortium, S.M.-I. (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol, 32, 903-914.
[2]Sahraeian, S.M.E., Mohiyuddin, M., Sebra, R., Tilgner, H., Afshar, P.T., Au, K.F., Bani Asadi, N., Gerstein, M.B., Wong, W.H., Snyder, M.P. et al. (2017) Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nat Commun, 8, 59.
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