Skip to main content

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