Mapping and quantifying mammalian transcriptomes by RNA-Seq.
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Cites methods from "Mapping and quantifying mammalian t..."
...A couple of methods were later developed that addressed the first problem by “rescuing” reads that mapped to multiple genes ("multireads”) [17,18]....
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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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13,356 citations
Cites background from "Mapping and quantifying mammalian t..."
...An important summary statistic is the number of reads in a class; for RNA-Seq, this read count has been found to be (to good approximation) linearly related to the abundance of the target transcript [2]....
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...A common feature between these assays is that they sequence large amounts of DNA fragments that reflect, for example, a biological system’s repertoire of RNA molecules (RNASeq [1,2]) or the DNA or RNA interaction regions of nucleotide binding molecules (ChIP-Seq [3], HITS-CLIP [4])....
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13,337 citations
Cites methods from "Mapping and quantifying mammalian t..."
...cDNA was prepared following a similar procedure to the one described in [17]....
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References
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"Mapping and quantifying mammalian t..." refers background in this paper
...These demands mean that it is not possible to use some tools that might be tenable in a small genome with few introns, such as BLAS...
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"Mapping and quantifying mammalian t..." refers methods in this paper
...Yeast and Arabidopsis thaliana transcriptomes have been profiled by RNA-Seq approaches concurrently with this stud...
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2,312 citations