Sentence examples for mapping quality filter from inspiring English sources
Raw reads were again aligned to the set of 3310 transcripts with a mapping quality filter of q = 55 to ensure mappings were unique.
A simple implementation of a mapping quality filter is implemented when possible to remove low quality mappings that could artificially inflate sensitivity (see Supplemental Materials S1).
Uniquely mapped reads were counted for each transcript on both strands with HTSeq-count [ 59] using a mapping quality filter of 30.
The mapping quality filter is applied to the anchor read only, as most aligners always attribute the lowest score to repetitively mapping reads.
Variation of the mapping quality filter (e.g. q as low as 10 or 20) resulted in only small changes in the coverage estimates.
The novel PEM-based and mapping quality filters are the main reason behind the reduced false positive rate in comparison to FREEC and CNAnorm (Additional file 1: Figures S1 and S3).
A parallel analysis relying on consensus base quality, quality of adjacent bases, and read mapping quality filters yielded similar SNP calls, but the fraction of the genome compliant with the analysis criteria was slightly reduced [Additional File 1: Supplementary Table S3].
After each run post-mapping quality filtering tools provided by JoinMap® 4 for the maximum likelihood method such as the plausible position matrix and the fit and stress monitoring were studied and markers causing a poorer fit were excluded.
While more stringent mapping quality filters can reduce these false-mapping rates, these filters would reduce the sensitivity of each of the other methods.
The set of read pairs that passed the above sequence and mapping quality filters was used to identify Alu insertion loci according to their position in the reference genome.
Default maq parameters were used for SNP calling and for filtering as described in the maq paper, (maq.pl SNPfilter -f cns.indelse -F cns.indelpe -d 3 -q 40 -Q 60 -w 5 -N 2), with a subsequent minimum map quality filter of 30 applied after the indel proximity filters.
