Figure 2

Number of genes assembled with a certain number of k-mer sizes and coverage cutoffs. a) For each of the 3,912 complete transcripts in the P. fastigiatum library the number of k-mer sizes (blue bars) and coverage cutoffs (yellow bars) leading to complete transcripts were counted. 721 genes were only assembled using one k-mer size and 501 using one coverage cutoff. b) Mean expression levels for genes assembled with a certain number of k-mer sizes and coverage cutoffs. For each set of genes that were completely assembled with the same number of k-mer sizes (red bars) and coverage cutoffs (green bars) a mean expression level was derived by computing the mean of the RPKM values (reads per kilobases and million mapped reads [30]). High positive Pearson correlation coefficients were found between the mean expression level and the number of k-mer sizes and coverage cutoffs.