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We only measured similar results when entity enhancement was left enabled at-runtime, which recompiles entity classes to a meta model on each read.
Data analysis was performed on each read sequence by computational tools, as constructed previously [20] with some modifications.
Therefore, different transformations are carried out on each read in order for them to be correctly processed.
HPG-Methyl adds some important contributions for processing bisulphite reads: first, different transformations are carried out on each read in order to correctly process them.
After library preparation paired-end sequencing was performed for 40 cycles on each read and images were processed using Illumina pipeline 1.4.
On each read sample we estimated the line PSG parameters with both JR and EM and calculated the distance between each method's estimates and its estimates on the full read set.
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In other words, the position of each read on the target genome, and thus positions of sequencing errors on the read are also present in the dataset.
All reads were quality filtered on the basis of each read containing a minimum of 90% of bases in each read having a minimum quality score of Q20.
For the simulated reads, we have computed the recall and precision measures since we know the true position of each read on the genome.
They should be able to find the true position of each read on a reference genome and ideally distinguish between technical sequencing errors and natural genetic variations.
To map the raw 44 or 75 nt pair-ended BS-Seq reads, the original reads were computationally converted to the alignment forms with the following steps: 1) observed cytosines on the forward read of each read pair were in silico replaced by thymines; 2) observed guanines on the reverse read of each read pair were in silico replaced by adenosines.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com