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The presence of a particular amplicon was associated with a large number of specific reads (as assessed by the genomic alignment of read tags) whereas its absence was associated with a lower number (or total absence) of specific reads.
Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers.
The posterior probability of methylation status is determined based upon the product of prior distribution of methylation and the likelihood of specific reads aligned to a site.
Amplicon libraries are sequenced, and reads matching the targeted locations are counted: a high number of specific reads indicates that the corresponding PCR reaction amplified the targeted TE junction and that the TE was present whereas the absence of specific reads (or the presence of a small number of cross-contaminating reads) indicates that the TE was absent.
Following these two quality control steps, passed E amplicons were finally checked for miscalls due to the presence of very short L1 or Alu elements resulting in large numbers of specific reads.
Thus, for each sample of each E amplicon, the genotype call was automatically set to absent (absent amplicon, i.e. L1 present) if the fraction of specific reads containing an L1Hs tag or AluYb8 tag was greater than 80%%.
Similar(52)
As a consequence, in case of specific reading behaviors where the reading order is preserved, the algorithm will have good performances.
Bias towards the line was calculated by taking the number of Line specific reads divided by the total number of allele-specific reads (Tester + Line).
Types of intervention and ideas range from the use of iPads, Kindles and other electronic devices to the use of blogs, guided reading, literacy leaders and the teaching of specific reading skills.
The counts were normalized using the total number of library specific reads.
The number of SASI specific reads varies between samples, but for each their representation roughly approximates the 0.1% spike-in level.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com