This is also the case when comparing lane passed filter (PF) rates and the percentage of PF reads where the average base call quality is above Q30, for lanes with similar number of generated reads (Figure S1).
The variation in the number of generated reads per sample remained unclear.
The final number of generated reads in all HMP, GOS and GNHM subsets together with the corresponding percentage of positive examples is shown in Table 1.
Reads were again generated, and treated as the dataset for the sample 2. To test the effects of sequencing depth, we varied the number of generated reads for each dataset from 1 to 50 million (M).
Despite this reduction in the mapping rate, we observed a high level of correlation between the number of generated reads and the observed mapped reads (r = 0.95, 0.96, 0.95 for A, B and D homoeologous triplets, Fig. 3).
Although high-throughput technologies allow users to make tradeoffs between read length and the number of generated reads, very little has been done to determine optimal parameters even for common applications such as RNA-Seq.
The large number of generated reads allows detection of low-abundant transcripts and the cDNA cloning step where mRNA molecules are inserted into bacterial vectors is no longer required [ 30].
The numbers of generated reads were 50 for 100 bps reads and 100 for 50 bps reads in a block to adjust the average coverage depth equals to 10. Also, we generated reads with designating error rate to 0%, 2 %, 4 %, 6 and 8%, in order to determine the dependency of manding results on read error.
The RNA-seq libraries were sequenced on the SOLiD5500xl system, generating reads of length 75 bp.
All simulation runs indicated that MEGAN generally is capable of binning the majority of all generated reads correctly.
