Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
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Cites background from "Transcript assembly and quantificat..."
...1883" language="eng" relation="no"> Recent advances in massively parallel cDNA sequencing (RNA-Seq) provide a cost-effective way to obtain large amounts of transcriptome data from many organisms and tissue type...
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14,524 citations
Cites background or methods from "Transcript assembly and quantificat..."
...of transcript i [6], given by ∑ x≤"i λF(x)("i − x + 1) for poly(A)transcripts and ∑ x≤"i+"A λF(x) min ("i + "A − x + 1, "i) for poly(A)+ transcripts, where lA is the length of a poly(A) tail....
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...The reads produced can be used for a number of transcriptome analyses, including transcript quantification [2-7], differential expression testing [8,9], reference-based gene annotation [6,10], and de novo transcript assembly [11,12]....
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...The use of a fragment length distribution for RNA-Seq quantification was first introduced by [6] for paired-end data and later described by [4] for single-end data....
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...Since the publication of the RSEM methodology, a number of methods utilizing similar statistical methods have been developed [3,4,6,19-22]....
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...The transcript fraction measure is preferred over the popular RPKM [18] and FPKM [6] measures because it is independent of the mean expressed transcript length and is thus more comparable across samples and species [7]....
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14,103 citations
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Cites methods from "Transcript assembly and quantificat..."
...Furthermore, because the number of reads produced from an RNA transcript is a function of that transcript's abundance, read density can be used to measure transcrip...
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References
83,420 citations
"Transcript assembly and quantificat..." refers methods in this paper
...Type I errors were controlled with the Benjamini-Hochberg [2] correction for multiple testing....
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...Between any two consecutive time points, we tested whether a transcript was significantly (after FDR control [2]) up or down regulated with respect to the null hypothesis of no change, with variability in expression due solely to the uncertainties resulting from our abundance estimation procedure....
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45,957 citations
Additional excerpts
...index) and RNA-Seq reads as FASTA or FASTQ and produces alignments in SA...
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"Transcript assembly and quantificat..." refers methods in this paper
...cDNA was prepared following a similar procedure to the one described in [17]....
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11,473 citations
"Transcript assembly and quantificat..." refers methods in this paper
...[24] Fragments were mapped to build 37....
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...We extended our previous algorithms described in [24] to exploit the longer paired reads used in the study....
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