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Differential gene expression between samples was quantified at the gene level using the read summarization program featureCounts (see Code Availability 3)2.
A. kamchatica reads were mapped to two parental species genome (A. halleri56 and A. lyrata) and separated into two groups using the read classification method HomeoRoq56, and we treated each A. kamchatica sample as two different diploid individuals.
We then compared the allele frequencies calculated using the read counts in the pools to the actual allele frequencies determined from the HM+1KG genotypes for each pool.
A novel probabilistic model was developed to identify and quantify genomes using the read mapping approach.
Rather, we estimate copy number state using the read count ratio after the CNV is detected.
Using the read data, we ascertained SNPs using a novel de novo assembly approach outlined in Ahiska (2011).
We then calculated Pearson's correlation coefficient (R) using the read counts for each HPG between every two segments.
Using the read amounts for each annotated isotig (from a total of 15,671), we identified 7,756 transcripts.
Comparable is defined as a score within one standard deviation of the best candidate using the read label score distribution for the read.
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Using the read-across method, Hartung's software compares a new chemical to closely related compounds and assesses the probability of toxic effects by reference to the properties of these known chemicals.
Fig. 10 The performance results of RUBiS using the read-write request transition type.
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