Sentence examples for mapping quality of from inspiring English sources

To get RNA-seq quality metrics, bedtools utility (http://bedtools.readthedocs.org) was used to overlap TopHat2 mappings with mapping quality of at least 20 and defined exons and introns with a minimum overlap fraction of.8.

Only uniquely-mapped reads were retained for subsequent analyses (mapping quality of at least 20 and perfect matches) (Li et al. 2009).

Alignment was performed with BLASR28 -bestn 3, and primary aligned reads with mapping quality of 254 were used.

For pooled SNP detection, we only considered reads with a MAQ mapping quality of 20 or more and with three or fewer mismatches to the reference sequence.

We attempted a variety of filtering schemes for SNP-calling, incorporating thresholds for consensus base quality, mapping quality of supporting reads, and consensus quality of adjacent bases.

The SAM tools package was used for SNP discovery using stringent parameters (e.g. minimum coverage of 8 reads and mapping quality of 20).

The alternative mapping quality of a predicted SV is the average mapping quality calculated over discordantly mapping read pairs within a cluster.

A minimum of 25 reads of mapping quality of at least 20 and base quality of 25 and above were required to report each variant.

Reads were mapped against the latest reference genome (assembly 10.2) using BWA [ 46], allowing 7 mismatches and filtering by mapping quality of 20.

Similar to GATK [ 18], only the mapped short reads with mapping quality of greater than 20 were considered, and only bases with base quality greater than 17 counted.

Parameters for the identification of indels included that they be mapped to both strands, had a minimum indel mapping quality of 50 and minimum mapping quality of 20 for the non-indel (anchor) tags, at least an average of 10 bp from the end read position, and a minimum coverage of 8X.