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Our findings are that primers designed for transcript regions of higher read coverage resulted in vastly improved detection of mRNA transcripts that were not previously detected or were not consistently detected in the same samples using conventional primers.
The coverage gradually increased, tracking expression level, with much higher read densities for the most highly-expressed genes (Wilcoxon-Mann-Whitney p = 10−16) (Figure 4, upper panel).
Reduction of pool complexity also generated higher read redundancy (Figure 4C), the error-correcting potential of which would permit lower mismatch tolerances during assembly, in turn reducing the probability of spurious joining (Figure 4D).
A sequencing bias toward higher read density in GC-rich regions has been demonstrated in the Illumina-based deep sequencing of the genomes of the plant Beta vulgaris and the bacterium Helicobacter acinonychis [22].
Moreover, we required the minor allele at each SNP be represented in at least three reads and that the total number of reads per SNP was lower than 120 (SNPs with higher read depth were discarded).
Pindel and PRISM particularly benefit from a higher read depth.
Diminishing returns are only seen at much higher read depths.
Additionally, in many tests of differential expression higher read count will result in higher statistical confidence.
All three methods obtain higher read counts for all evolutionary distances.
Interestingly, some miRNA*s had higher read numbers than the corresponding miRNAs.
These repeat regions were independently supported by locally higher read coverage.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com