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Commonly one probe set from one species maps to multiple probe sets from a second species.
SNP rs3873375 was removed because it maps to multiple genomic regions and shows 4 distinct genotype clusters.
If F (x i )maps to multiple values of Y, then the data are mapped to the set of nodes, { y ∣ y = F (x i )}.
Anticipating this problem, we chose to perform paired-end sequencing, which allows a read pair to be unambiguously mapped if one end can be unambiguously mapped, regardless of whether the other end maps to multiple locations.
Every reagent that maps to multiple genes is shown with phenotype terms assigned, but in this case due to the off-target effect (Guest et al., 2011) we cannot know which phenotypes are associated to which genes, therefore the corresponding genes do not have phenotypes displayed.
In their recent RNA-seq study of X A ratios, Xiong and colleagues [ 19] implemented what has been termed "unique" mapping parameters to map their datasets, meaning each short sequence read is aligned to the best position in the genome while any read which maps to multiple positions is excluded from the output.
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Other 629 TFs showed multiple (many probesets mapped to single locus) or ambiguous (single probeset mapped to multiple loci) mappings.
Additionally, 34.77%, 19.28%, and 28.97% of reads mapped to multiple loci (multiply mapped reads) in Pt_v1, Pt_v2, and Pt_v3, respectively.
For reads mapping to multiple loci, upstream and downstream DNA sequences were obtained from one mapped site selected at random.
Reads mapping to multiple genomic positions were removed.
If a read or reads pair is mapped to multiple positions, BWA will choose the most likely placement.
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