Only sequences with unambiguous reads were compiled into data sets and were aligned with the closest sequence relatives from GenBank database by using Kodon.
Transcript expression levels were computed for each treatment/time point sample independently as the unique (i.e. unambiguous) reads per kilobase per million reads (RPKM).
Using the CLC Bio Transcriptomics Analysis tool, de novo assembled transcript counts for paired reads were normalized by calculating the number of unique (i.e., unambiguous) reads per kilobase of exon model per million mapped reads (RPKM) (Mortazavi et al. 2008).
Thus, for appropriate comparison and alignment, the msp2 5´ sequences were edited from the positions where unambiguous reads could be determined and terminated 70 nt into the sequence at the approximate beginning of the hypervariable region.
Estimating isoform expression levels based solely on unambiguous reads, as suggested, e.g., in [ 2], results in splicing-dependent biases similar to the transcript-length bias noted in [ 11], further complicating the design of unbiased differential expression tests based on RNA-Seq data.
Because aligned grid-cell lattices with perfectly periodic tuning curves imply that the posterior is periodic too (compare Equation 8), information from different scales would have to be combined to yield an unambiguous read-out.
In particular, we wrote: "Because aligned grid-cell lattices with perfectly periodic tuning curves imply that the posterior is periodic, too (compare Equation (8)), information from different scales would have to combined to yield an unambiguous read-out.
However, Consortium for the Barcoding of Life (CBOL) disregarded trnH-psbA as it does not consistently provide bidirectional unambiguous sequencing reads [17].
Gene expression levels were calculated based on read counts which also included unambiguous mapped reads according to negative binomial distribution.
