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We used the identical coordinates as in our previous study (Herz et al. 2012) based on an fMRI study by Haslinger et al. (2001).
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Hits were restricted to those with 100%% similarity, 100%% coverage of our query or of the subject sequences of the databases, and with identical coordinates in the genome.
Interestingly, these studies all show that affected members of eleven FAP kindreds in the United States share the promoter deletion with identical coordinates.
After removal of all but one of the reads mapping with identical coordinates and orientation (potential PCR duplicates), the remaining reads were remapped using the MAQ software package [ 24].
We edited the xml file, prior to analyses, to input random noise to offset identical coordinates using the jitter option with a parameter of 0.01.
For paired-end data this option uses Picard tools (http://picard.sourceforge.net/) to 'collapse' multiple read pairs that have identical coordinates for the first and second read into a single representative pair.
Further investigation using Sanger sequencing confirmed the identical deletion coordinates in both probands.
Two types of duplicates were identified and flagged: records with identical coordinates –true duplicates and those records that fall in the same grid cell of the environmental spatial layers – geographical duplicates.
We enforced the Jitter option on multivariateTraitLikelihood to add a random noise to samples with identical coordinates.
Only events with identical coordinates of an alternatively processed intron(s)/exon(s) were regarded as completely conserved.
Reads having identical coordinates were collapsed into a single read, and reads with mapQ > =10 passed to FindPeaks 3.1 [ 80] (with a fixed directional read extension of 300 bp) for generation of an unthresholded coverage WIG file to be visualized in the UCSC genome browser [ 81].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com