Sentence examples for the alignment rate from inspiring English sources
Unfortunately, despite these steps, the alignment rate of each aligner was significantly lower than expected, so to offset this, the fastx toolkit was used to filter out low quality reads (Table 1).
For AzoCH3, the alignment rate increased along with the increase of the content of SNPs, showing that the alignment rate, at least for "fast" process, could be enhanced by doping SNPs.
For AzoCN, the alignment rate decreased with the increase of SNPs concentration, and when the SNPs' concentration achieved 0.24% the ratio of alignment rate reached the minimum, about 77% of that of the undoped sample.
Above and beyond all other factors controlled for, the LAO variable itself is significant at the 95% confidence level, providing strong evidence that LAO significantly improves the alignment rate.
This approach limits consideration to known SNPs, but equalizes the alignment rate of reads containing known variants.
The effect of adapter sequences is also more serious, given the risk of incorporating adapter sequences into the final sequence assembly, compared with the mere reduction in the alignment rate typically seen in reference-based approaches.
The alignment rates of the reads generated from the 12 samples which mapped against the pseudo-reference range from 67.21 to 85.31 % while the alignment rates range from 66.11 to 84.19 % if the reads were mapped against the original MSU7 cDNA sequences.
The increase in the alignment rates shows that extra information was incorporated in the pseudo-molecule sequences by modifying the SNP and InDel sites.
Additional file 1: Table S1 shows the alignment rates for all samples.
According to the alignment rates shown in Figure 4a, all methods work with almost the same number of mapped reads when Bowtie2 is used.
This explains the weak agreement of same transcript estimates between pairs of replicates reported for BitSeq in Rossell et al. (2014) and is a reminder that it is very important to check the alignment rates.
