Sentence examples for trimming parameters from inspiring English sources

The results of simulation studies are presented to discuss the influence of different copula models and different trimming parameters.

Table 1 shows how trimming parameters influence the average length and quality of the reads used for mapping.

Trimming parameters for each data set were specified after quality control using the NGS QC toolkit (Patel and Jain 2012, supplementary table S1, Supplementary Material online).

The pre-processing function returns statistics and figures describing read qualities by read position, and these outputs enable users to set trimming parameters.

Vector clipping, quality trimming and sequence assembly using stringent conditions (e.g., high quality sequence trimming parameters, 96% sequence identity cutoff, 35bp overlap) was done with the Lasergene software package (DNAStar Inc).

Alignments were trimmed using trimAl (version 1.2rev59 with trimming parameters set to "automatic") [ 71] and phylogenetic trees were reconstructed using PhyML (version 20120412) [ 72] using the WAG model for amino-acid replacement and BIONJ as starting tree.

The ARF method includes two parameters: a trimming parameter t, which determines the percentage of the values used in fitting the regression model, and a Boolean parameter a, which indicates whether or not to include an intercept term in the regression model.

All default parameters were used while mapping reads using BWA except for the read trimming parameter.

Sequencing reads were aligned to the current human reference sequence (assembly hg19, NCBI build 37) (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/) by using Burrows-Wheeler Aligner (BWA version 0.6.1, http://bio-bwa.sourceforge.net/, Li and Durbin) with a read trimming parameter – q of 20.

The investigation of the Drosophila circadian model illustrates the dual perspective that comes from our approach: (i) helping experimental biologists by showing the consequences of their assumptions and (ii) leading modelers to refine their models by trimming unnecessary parameters.

Quality filtering was performed using Trimmomatic (v0.25) [ 70]: low quality reads were trimmed if average Phred quality scores were less than 20 within a 3-bp sliding window and discarded if the length was below 40 bp after trimming (Trimmomatic parameters: SLIDINGWINDOW 3 20 MINILEN:40).