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After trimming 108 bp from the ends of each contig, where a reduction in mapped read coverage would be expected, the median coverage of mapped reads was 19× (mean = 18.94×; SD = 10.42).
Degrading the grid resolution of the LiDAR data from 1 m to 10 m resulted in a disagreement in mapped contributing areas of between 29.4% and 37.3% of the study area, depending on the DEM conditioning technique.
In RNA-seq experiments, this reduction in mapped reads leads to underestimation of expression level of genes with variations (4).
The reduction in mapped TSS genes is a result of minor annotation differences between the papers and the Affymetrix GeneChips™.
The transcript abundances of alleles derived from each parent were estimated using polymorphic sites in mapped reads in the hybrid.
The changes in Ct value were approximately two- to threefold higher in mapped DHSSs compared to random sites (Fig. 2c).
In order to reduce Poisson noise in mapped read-counts we only considered captured fragment read counts greater than a threshold (5 reads per restriction fragment).
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An average of 97.3% of the reference was mapped with a mean depth of 53.3-fold in mapped regions across all isolates (Supplementary Table 1).
An average of 91.7% of each strain was mapped using SMALT with a mean depth of 118.6-fold 118.6-foldn mapped regions acoveragel inolates, as previously described (14).
Differences in derived contributing areas and flowpaths among various conditioning techniques increased substantially at finer grid resolutions, with the largest disagreement among mapped contributing areas occurring between the 1 m resolution DB DEM and the SB DEM (37% disagreement) and the DB-DF comparison (36.5% disagreement in mapped areas).
Illumina reads for each isolate/line were mapped to the B. xylophilus reference genome (ver. 1.2) using SMALT v0.7.4 (https://www.sanger.ac.uk/resources/software/smalt/), with options –x (each mate is mapped independently) and –y 0.8 (minimum 80%% of the read length matches in mapped reads).
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