However, the method in [9] exploits edge detection to identify brushstrokes, whereas the proposed technique relies on repeated thresholding and validation steps.
Foley has a final thought that is worth repeating: "Threshold will include updates to all three Windows OS platforms (Xbox One, Windows and Windows Phone) that will advance them in a way to share even more common elements".
Alternatively, an increase of the copy number repeats threshold to 4 or 5 instead of 3 removed most of these false hits but it will also decrease significantly the sensitivity of the pipeline.
As long as the duplicates are below a repeat threshold (50 alignments by default), all seeds are continued through until the filtering part of the algorithm; duplicate junction locations for a read are resolved at that point.
Msatfinder v. 2.0.9 [ 53] was used to identify simple sequence repeats (SSR), with the following settings: a six-repeat threshold for mono-nucleotide SSRs, a five-repeat threshold for di- and tri-nucleotide SSRs and a three-repeat threshold for tetra-, penta- and esa-nucleotide SSRs.
Parameters: mer length = 5; mer repeat threshold = fixed, 150; read assignment qualification - match 80%% of read or 20 bases.
All the unique sequences were used to search for microsatellite makers using Msatfinder [ 31] with a repeat threshold of eight di-nucleotide repeats or five tri-, tetra-, penta-, or hexa- nucleotide repeats.
Additionally, none of the CGG KI mouse models show any evidence for Fmr1 promoter silencing, so none of the mice show the dramatic reduction in gene expression at the 200 230 CGG repeat threshold often described in human studies.
