Sentence examples for minimum depth threshold from inspiring English sources

Additionally, RNA-seq reads from all infected replicates (both IL and IP) were combined to create a "pooled infected" library, and ShortStack analysis was repeated to obtain 187 total clusters meeting the minimum depth threshold (Table  2).

This was done at different minimum depth thresholds (8-fold, 12-fold, and 16-fold).

We therefore examined the effect of different minimum depth thresholds (8-fold, 12-fold and 16-fold) on the false positive rate of SNPs identified under the Maq-120 analysis.

SNPs were called using SAMtools 0.1.18 [ 22] with a minimum read depth threshold of 6 and then compared with genomic reads using BEDTools 2.17.0 software [ 23].

Read-type specific raw variant lists were filtered by the SAMtools varFilter.pl utility by setting a minimum read depth threshold of six and a maximum read depth threshold of 200.

In order to ensure sufficient allele sampling, as well as to prevent sequencing errors from appearing to be actual variants, all four studies use or recommend a minimum sequence depth threshold, ranging from 8- to 30-fold depth of coverage.

A '?' indicates an uncertain hit, where only one end (left or right of the predicted insertion) passes the minimum read depth threshold; this often occurs when the IS is inserted within or adjacent to a multi-copy sequence, as described above (Fig.  2).

Despite the observation that many genotype calls are supported by >20 reads, the number of SNPs for downstream analysis declines rapidly as the minimum depth of coverage threshold is increased from 1 to 10 while implementing a missing data threshold of 20%.

We further reduced the number of markers to 3967 SNPs by applying a minimum depth of coverage threshold of six sequence reads for a genotype call (i.e., any genotype with fewer than six supporting sequence reads was set to missing) and then re-filtering for SNPs with <20% missing genotypes.

When the minimum depth was lower than the threshold or the robot location did not change for a period of time, we set the robot state to a termination and robot was reset to the start position.

In each iteration, short contig c is removed if its depth T(c) is lower than the minimum of cutoff threshold t and the depth threshold β.