However, in order to filter out artifactual false positives, the ME-Scan pipeline discards loci that lack the expected Alu sequence, and so these loci lead to false negative results.
Longer reads would increase both the sensitivity and specificity of the ME-Scan analysis pipeline.
In the current ME-Scan analysis pipeline, Alu insertions are treated as presence or absence states for purposes of comparison.
The ME-Scan analysis pipeline described above depends on mapping reads to a reference genome for two reasons.
A PiB SUV ratio cut-off point of 1.4 is consistent with a 90% sensitivity of clinically diagnosed Alzheimer's disease subjects with an abnormal PET scan using our pipeline (Jack et al., 2014).
The mixture model pipeline scans for AEI signals at the SNP level, while the whole gene filtering method scans for AEI signals at the gene level; 2. For the whole gene filtering method, the read ratios of SNPs in all genetic regions (3' UTR, exon, intron, and 5' UTR, etc).
The PICRUSt pipeline scans KEGG functional database and uses the OTU table of assigned taxa and their relative distribution to generate the relative abundance of functional categories.
As the automated pipeline scans literature for URLs, names and other unique identifiers of resources, it is able to report where and when a resource has been cited, regardless of whether a literature citation to the resource was included, information currently not available to resource providers through existing scientific websites (i.e. Web of Science, PubMed).
We constructed a comprehensive bioinformatics pipeline to scan for fetal chromosomal aneuploidies.
We have used an EST-based pipeline to scan for differential gene expression levels between normal and tumor states.
We have used an EST-based pipeline to scan for UTR-located polymorphisms associated with libraries of cancerous origin.
