NY 348 and the Northway did not connect, as NY 348 crossed under the four lane expressway, crossing the alignment of a railroad spur and soon reached the hamlet of Chazy.
However, due to cross-alignment of probes, we cannot unequivocally assign cDNAs from the duplicate copies to a specific locus.
The genomic regions where the GS genes were located were examined in detail by determination of the open reading frames (ORFs) upstream and downstream of the specific GS genes and cross-alignment of these adjacent regions between the gene pairs.
Ordinarily this could result in cross-alignment, i.e. wild type reads derived from a given barcode could potentially be mapped to an incorrect barcode closely neighbouring in address space.
Our simple implementation was to replicate the barcode four-fold ("munging") such that a one base difference became amplified to four, thus defeating cross-alignment by Maq with default parameters.
For these genes, there are indications of differential expression in non-brain tissues by RNA-seq, although we cannot unequivocally demonstrate brain expression due to cross-alignment of cDNAs to multiple loci (Table 1).
At East Main Street, NY 31 resumed its eastward alignment, crossing the Genesee River and continuing on Main Street to Monroe Avenue, which, at the time, connected directly with Main Street.
However, the aligner fails to find the proper alignment because it does not consider all possible alignments crossing splice junctions owing to the search complexity.
The number of alignments crossing the junction is divided by the coverage of the more deeply covered side to obtain an estimate of the minor isoform frequency.
The alignment crosses a deep gorge of the Chenab River, which necessitates construction of a long-span railway bridge.
