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Table 5 Comparison of mouse transcripts assembled using MapReduce-Inchworm or the original Inchworm with a reference mouse transcriptome

From: K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity

 

alignment cutoff

MapReduce

Original

Number of reference transcripts recovered

95

6230

6231

90

12,198

11,600

85

14,912

14,546

80

17,340

15,995

Number of transcripts that map to reference

95

12,627

13,601

90

24,816

24,770

85

30,923

32,397

80

33,966

35,208

  1. Statistics from the REF-EVAL component of DENONATE [41] using mouse RNA-seq data [22]. Dividing the number of reference transcripts recovered by the total number of reference transcripts (22402) gives the Recall shown in Fig. 3(b). Dividing the number of transcripts that map to reference by the total number of assembled transcripts (78,719 for MapReduce-Inchworm and 80,825 for original Inchworm) gives the Precision shown in Fig. 3(d). The recovery rate was measured at the contig level, which requires certain amount of complete alignment in a one-to-one mapping between the assembly and the reference. Alignment cutoff refers to the minimum required alignment for the recovery rate calculation. MapReduce refers to the results of Trinity run with the MapReduce-Inchworm method presented here. Original refers to the results of Trinity run with the original version of Inchworm