Sentence examples for minimum alignment counts from inspiring English sources

Fold-change calculations were undertaken between wild type and cgrA deletion strain samples at 24 h in CENBA medium using Cuffdiff with geometric library normalization method and minimum alignment counts of 10.

Fold-change calculations for time course expression were undertaken pair-wised between samples of 4 hours in CENBA medium and sample at 24, 48, 72 and 96 hours in CENBA medium using Cuffdiff with geometric library normalization method and minimum alignment counts of 10 [ 74, 75].

The minimum alignment count per locus was set to 20 (-c option).

Differential expression was determined between OP and CP samples with Cuffdiff using a minimum alignment count of 500 [ 33, 34].

Default parameters for Cuffdiff were used except the minimum alignment count was set to 2 and FDR set to 0.01.

Transcripts were assembled and quantified by Cufflinks v2.0.2 [ 64, 65] with a minimum alignment count per locus of 20.

Quality control and reads statistics were determined with FASTQC http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/. Transcript assembly was performed using Cufflinks v0.9.3 [ 59], with a minimum alignment count per locus of 10.

Differential gene expression analysis was performed using Cufflinks, Cuffcompare and Cuffdiff (Trapnell et al., 2012), setting the false discovery rate threshold for significance at q = 0.05, the minimum alignment count to 10 and including quartile normalization (http://rsbweb.nih.gov/ij).

The variable and relatively low coverage of the wDi transcriptome in some life cycle stages required certain parameters be adjusted (the minimum alignment count to be lowered) in order to conduct differential expression significance testing.

¥ Lowest common ancestor (LCA) using 1e-5 cutoff, 60% minimum identity, and a minimum alignment lenght cutoff of 15.

This search identified 708 hits (E<e−10, identity ≥ 70%, and minimum alignment length >50 bp).