Sentence examples for mapping quality reads from inspiring English sources

We then ran samtools mpileup with the -C50 option to filter for high mapping quality reads.

Alignments with mapping quality <30 (mapQ < 30) were skipped to down-weight the contribution of the low mapping quality reads.

Alignments were filtered to remove low mapping quality reads and redundant duplicate reads were filtered out using the Picard MarkDuplicates Tool 1.85 (http://broadinstitute.github.io/picard).github.io/picard

Second, directly filtering low mapping quality reads reduces the signal-to-noise ratio (SNR) of the RC profile [ 23] so, instead, seqCNA provides a filter that discards windows, based on the mean mapping quality of proper reads.

CNV calls were filtered using stringent criteria including P-value <0.01 and size >1 kb, and calls with >50% of q0 (zero mapping quality) reads within the CNV regions were removed (q0 filter).

The binary alignment format (BAM) files used for CNV analysis were filtered based on mapping quality (reads with MAPQ < 20 were discarded), and processed using CNVrd2 [ 32] (v1.4.0), where the read-depth was counted in 3000-bp non-overlapping windows.

Base quality, mapping quality, read depth and tumour cell content are summarised in Supplementary Table 6, and further details of the bioinformatics approaches are given in the Supplementary Methods file.

After alignment to the reference genome, low-mapping-quality reads were discarded [mapQV (<10)] and unique reads were associated with known genes based on UCSC annotations, and the number of reads aligned within each gene was counted.

After filtering low-mapping-quality reads [mapQV (<10)], most of the reads were mapped on exons (27 41%), and many were mapped on intergenic regions (25 33%) (Table 1), indicating potentially unannotated expressed genes in the pig genome.

We identified single nucleotide differences with Samtools[ 13] (v.0.1.9), and filtered out potential false positives by mapping quality and read depth (based on the different sequencing depths for the samples).

Reads with mapping quality <20 and reads which were marked as duplicates by Picard v1.65 were excluded from further analysis.