We also excluded related individuals using the grm-cutoff command in GCTA [ 16] with a value of 0.025 (i.e., removing iteratively one of a pair of individuals with a relationship coefficient larger than 0.025).
In detail, to predict miRNA binding sites, we applied miRanda v3.3a with the default pairing score cutoff of "≥140" and "–strick" command, which only considered stringent 7-nt seed pairing (requiring an uninterrupted match of at least seven nucleotides from the 5'-end of the miRNA).
SNP filtering was performed in two steps, first using SAMtools'varFilterer' command specifying fairly permissive minimum quality cutoffs, coverage depth min/max cutoffs of 4 and 100, as well as options to disqualify SNPs that are too close to each other (as required by Illumina's GoldenGate Assay).
The sequence files and qual files were extracted using PHRED [ 18] with a command line option –trim_alt and a cutoff parameter of 0.1.
To assign sequences into OTUs, a further neighbor-clustering algorithm was employed using the cluster command in MOTHUR, with 97% sequence similarity as the designated cutoff.
For network representations in cytoscape (version 3.1.1; Shannon et al. 2003), protein diversity was first reduced by clustering all sequences with the usearch program (Edgar 2010; search performed using the -cluster_fast algorithm with a cutoff of -id 0.XX as given in the respective figure legends; the –centroid command was used to obtain the sequences).
These cutoff frequencies are 20 and 120 kHz, and can be selected by the telemetry command.
Transcripts were clustered using cd-hit-est command in CD-HIT v4.6.1-2012-08-27 [ 53, 54] with > 95% similarity cutoff and only the representative transcripts in each cluster were retained.
To compare pregnancy outcomes between multiple hemoglobin cutoffs in the same time, summary data of hemoglobin cutoffs and outcome groups were then expanded to individual patient data using the expand command in STATA.
Mendoza subsequently lost command of his fastball and hit a couple of batters, and when Ledee overthrew a cutoff man, it allowed Toronto to score four runs in the inning, rather than three.
And for those who do not cooperate, here are the consequences for you: whether it's public criticism, cutoff of contacts, no more phone calls, all the way up to whatever instruments the United States has at its command".
