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The comparison between the two techniques resulted in 32% more reads for α, 7% more reads for β, 36% more reads for γ and over three times more reads for δ using RNAseq compared to ESTseq.
These examples are representative of a subset of loci selected by virtue of having five or more reads for at least one of the P4R2 species at the locus in wild-type (Col-0) plants.
Above all, motif enrichment provided many more reads for these loci, making it possible to detect the polymorphism in flanking regions of particular interest for primer design [ 34- 36].
For a simulated positive control, we generated a simulated data set of 2 million 10-codon reads over coding genes, but we biased these simulated reads to give more reads for the codon AAA at position 6 of the footprint.
While the exon-rich regions had more reads for exons than introns or intergenic regions, the exon-sparse regions had similar numbers of intronic and intergenic reads as the exon-rich region.
This strongly suggests that using the Illumina platform, which can provide two orders of magnitude more reads for less than half the cost of the current 454 technology, is the best way forward for quantitative expression analysis.
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C4-P2 chemistry was chosen because it favours long, more accurate reads for de novo assembly.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com