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The markers were manually placed (in T4 and F8 channels) at the peak of the negative phase, but imprecise markings were later corrected by automatically shifting them to the largest negative peak within a predefined neighborhood (equal to the defined detection latency) around the original marking.
Co-segregating markers were manually determined using this display and defined as a "filled bin" [25].
New (i.e. not contained in the GWAS Catalog) association markers were manually tested on compliance with the criteria for inclusion in the GWAS Catalog before insertion in the candidate list.
Cells expressing each one or both markers were manually quantified and normalized to the total amount of Hoechst+ nuclei in the field and expressed as the means±S.E.M. Number of cells lacking the expression of both markers was calculated.
If no CAPS were previously designed from our SNP set, CAPS markers were manually designed with CAPS Designer (http://solgenomics.net/tools/caps_designer/caps_input.pl) and Primer3Plus (http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi/).
Similar(55)
All these markers are manually extracted.
Separate channels for each marker were manually threshold in ImageJ, and the 'Analyze Particles' function was used to measure areas for each in all focal planes collected.
In the zoomed window, the centre of each reflective marker was manually selected.
In addition to quality control via call rate and Hardy Weinberg, the histogram plot for each marker was manually evaluated, and a total of 15 markers showing aberrant patterns were excluded.
During BAC anchoring, the contigs showing conflict in the marker-BAC relationship were manually split based on CB map and BES information.
The genotype profiles produced by SSR markers were scored manually.
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