To minimize the artifacts of ambiguous mapping, we retained only those siRNA loci with more than three reads in at least two libraries.
After mapping, we retained for further analysis only ESTs, which contained at least two exons, were mapped with overall 95% identity, and whose every exon was mapped with at least 98% identity to the human genome.
Because we were able to retrieve bases prior to each mapped position, we retained a multi-mapped read if more than 90% of the mapped positions had the same prior four bases (Additional file 1: Figure S1, step 5).
To exclude the effect of mapping bias, we retained only the 241,729 targets on which the number of reads mapped using the two mapping strategies was the same in all the three simulated datasets.
To maximize the number of high-quality, true polymorphisms in our linkage map, we only retained putative polymorphisms for linkage mapping if they met several strict criteria, including showing missing genotypes in no more than eight offspring, not showing >85% of offspring with the same genotype, and having informative parental genotypes consistent with segregation in the offspring.
We retained map 1, on which we positioned, as accessory markers, the additional loci mapped in map 3. The position of each accessory marker relative to its most probable location was determined on the basis of the two-point LOD scores and recombination frequencies available from the 'Maximum linkage' table of JoinMap.
To determine if multi-mapped reads influenced the break preference at "ACGT", we retained uniquely mapped reads only (899 reads) and counted all of the possible 4-mer sequence of "xxxx▼" in the stitched reads as we had done previously.
Duplicate Genes: For multiple probesets mapping to the same gene, we retained the probeset with the maximum median expression value.
As no reference to static meshes can be stored, which is usually contained in UE4's "uasset" file format, the triangular data is retained inside the map we are importing into.
Over the years, Andersonville, a neighborhood that sits far north on the Chicago city map, has retained its mom-and-pop charms.
