Dear SEQanswers community,
does anyone know a study where the required sequencing depth/number of mapped reads is estimated for different sequencing technologies (454, Illumina, ABi) that allow identification of N% of the unique transcripts in the human genome? In other words, which depth would be needed to have a 95% coverage of unique transcripts in my human sample? It strikes me that there does not seem to be a published consensus on the depth we need to reliably identify (nearly) all transcripts. It seems to me that this kind of information is necessary for deciding if we can multiplex several samples within a run, as well as for estimating the suitability of long-read technology for whole-transcriptome RNA-Seq.
Literature on the topic seems to be sparse: while reference [1] indicates that up to 80 Million ABi reads in mouse could be necessary before the number of different transcripts that have been identified reaches a plateau, study [2] suggest that about 3 Million mappable Illumina reads from human are required before the discovery rate flattens. Does anyone know equivalent data for 454, or could share some more comprehensive insights on this problem?
[1] Wang et al. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) vol. 10 (1) pp. 57-63
[2] Li et al. Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci USA (2008) vol. 105 (51) pp. 20179-84
does anyone know a study where the required sequencing depth/number of mapped reads is estimated for different sequencing technologies (454, Illumina, ABi) that allow identification of N% of the unique transcripts in the human genome? In other words, which depth would be needed to have a 95% coverage of unique transcripts in my human sample? It strikes me that there does not seem to be a published consensus on the depth we need to reliably identify (nearly) all transcripts. It seems to me that this kind of information is necessary for deciding if we can multiplex several samples within a run, as well as for estimating the suitability of long-read technology for whole-transcriptome RNA-Seq.
Literature on the topic seems to be sparse: while reference [1] indicates that up to 80 Million ABi reads in mouse could be necessary before the number of different transcripts that have been identified reaches a plateau, study [2] suggest that about 3 Million mappable Illumina reads from human are required before the discovery rate flattens. Does anyone know equivalent data for 454, or could share some more comprehensive insights on this problem?
[1] Wang et al. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) vol. 10 (1) pp. 57-63
[2] Li et al. Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci USA (2008) vol. 105 (51) pp. 20179-84
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