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After clustering the alignments by exon-exon junction, we implemented a filtering process to reduce the incidence of false positives due to poor alignments.
Also, aligning to a reference that differs too much from the reads may result in reference bias in variant calling or spurious variant calling due to poor alignments [ 4].
To reduce the incidence of false positives due to poor alignments, we implemented a filtering method based on the consistency of matches and mismatches on both sides of the exon-exon junction, essentially requiring that at least one read have a match to the genome at all 11 bp on both sides of the junction.
To avoid artifacts due to poor alignments between the mRNA and the EST sequences, only alignments with a percentage of nucleotide identity equal to or greater than 97% and with a length of the EST sequence aligned with the mRNA greater than 49% of the total EST length were selected.
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These composites show low levels of reinforcements due to poor alignment of GNS within the matrix as predicted by the modified Halpin-Tsai model.
Clusters yielding large Ka/ Ks ratios were checked manually to eliminate spurious results due to poor alignment.
This was mainly due to poor alignment of students' individualised training programmes with the rigid scheduling of evaluations.
Regions of detected recombination were checked for spurious signals due to poor alignment, mapping, contig joins or low quality sequence.
A further 499 OGs were removed from all subsequent analyses due to poor alignment and/or ambiguous orthology.
Since the algorithm detects peaks according to intensities (starting with the most-intense peak), this number might have to be increased in order to ensure that the non-detection of low-intense spikes is due to poor alignment and not due to the low intensities.
In negative studies without a strong process evaluation, it is difficult to discern whether the result was due to poor alignment of the intervention components with the causes of the problem leading to poor efficacy (theory failure) or due to a failure to implement the intervention as designed (implementation failure).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com