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Fig. 1 | Genome Biology

Fig. 1

From: Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts

Fig. 1

Equivalence class and transcript-compatibility counts. This figure gives an example of how reads are collapsed into equivalence classes. Each read is mapped to one or more transcripts in the reference transcriptome; these are transcripts that the read is compatible with, i.e., the transcripts that the read could possibly have come from. For example, read 1 is compatible with transcripts t1 and t3, read 2 is compatible with transcripts t1 and t2, and so on. An equivalence class is a group of reads that is compatible with the same set of transcripts. For example, reads 4,5,6,7,8 are all compatible with t1, t2, and t3, and they form an equivalence class. Since the reads in an equivalence class are all compatible with the same set of transcripts, we simply represent an equivalence class by that set of transcripts. For example, the equivalence class consisting of reads 4,5,6,7,8 is represented by {t1,t2,t3}. Aggregating the number of reads in each equivalence class yields the corresponding transcript-compatibility counts. Note that in order to estimate the transcript abundances from the transcript-compatibility counts, a read-generation model is needed to resolve the multi-mapped reads

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