Sequencing depth and coverage: key considerations in genomic analyses
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...While some authors will argue that as few as five million mapped reads are sufficient to quantify accurately medium to highly expressed genes in most eukaryotic transcriptomes, others will sequence up to 100 million reads to quantify precisely genes and transcripts that have low expression levels [7]....
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...Thus, sequencing samples at high depth (>80 million reads per sample) [23], which has been reported to improve the quantification of rare transcripts, may improve the accuracy of MCP-counter estimates from RNA-sequencing samples....
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Cites background from "Sequencing depth and coverage: key ..."
...Results: Qualimap 2 represents a next step in the QC analysis of HTS data....
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1,147 citations
Additional excerpts
...In 24 order to prevent this bias propagating to the quantification estimates, it is common to remove reads 25 or read pairs with the same alignment coordinates as they are assumed to arise through PCR 26 amplification of the same molecule (Sims et al. 2014)....
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References
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