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High throughput sequencing data poses a challenge to these studies due to the ambiguity in assigning short reads mapping to more than one genomic location (referred to here as multi-mapping reads).
In this chapter, we extend systems mapping to more complex and more heterogeneous structure of drug response by implementing stochastic differential equations (SDE).
A post-analysis manual filtering was performed for sequences mapping to more than 10 loci in genome, as well as telomere-associated loci, leading to the deletion of 123 loci from the 1015 initial loci reported in ta-si Prediction tool outputs.
Ambiguous tags mapping to more than one RefSeq gene were excluded.
Reads mapping to more than one genomic sequence were randomly assigned to one of these locations.
Following this step, data points were filtered out based on SNP call rate, call reproducibility, or marker specificity (i.e. markers mapping to more than 4 locations in the hg18 build of the human reference genome) as in Oldridge et al 2010 [16].
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The methods currently apply to ensure the robustness and dependability of software system do not effectively map to more open, dynamic environments.
Probe sets that mapped to more than two different Ensembl genes were discarded.
Since several pathways were mapped to more than one dataset, these pathways could be ascertained with high confidence.
In cases were a mRNA/cDNA/EST mapped to more than one gene, the best mapping was considered the correct one.
This accounts for cases when ProteinPilot assigned more than one unique accession to a given peptide (i.e. mapped to more than one place in the genome).
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