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According to van den Berg's statistics (Van den Berg et al. 2004), within Shell EP Europe alone roughly 1,200 footprint points had been registered in geotechnical and footprint datasets.
All of these were identified in the mRNA and total footprint datasets above as having genomic polymorphisms.
Together, the mRNA and footprint datasets identified a total of 10 nucleotide positions whose mismatch rates significantly exceeded the average.
Because both types of events would be represented in our data as mismatches between read alignments and the reference transcript sequence, we counted the total number of matching and mismatching reads covering each nucleotide position in each stop codon in our mRNA-seq and ribosome footprint datasets.
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An ALS survey was completed in early 2014 using an Optech Pegasus scanner to collect a discrete, small footprint dataset.
It was detectable in the CORG footprint dataset because of its location upstream of a conserved putative gene C14orf87 with unknown function.
Under the null hypothesis that A-to-I editing drives readthrough, one would expect nearly all footprints (for our purposes, conservatively assuming 90%) in the A-site footprint dataset to contain an edited base.
Under this assumption, we used a binomial test to estimate the probability of observing the proportion of A-to-G mismatches in the A-site footprint dataset at each adenine residue sufficiently covered by reads (217 positions, representing roughly 50% of A positions in all readthrough events reported).
We evaluate this approach by comparing the accuracy and overall quality of extracted buildings to a building footprint control dataset.
To improve our sensitivity in detection, we re-aligned our footprint and mRNA datasets to a Bowtie database of spliced transcript models, allowing three mismatches (where we previously only allowed two).
Although downsampling of the original MR data was necessary to reduce the memory footprint of the dataset as well as to introduce a uniform smoothing, which improved the performance of the segmentation algorithms, it also inevitably introduced small distortions to geometrical structures.
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