We're not sure, but HairMax, the manufacturer, says that 93% of affected men who used the product showed increased hair thickness and strand counts.
countOverlaps is also used to determine the number of reads overlapping a gene on the same strand (counts).
For LoFreq, the results of applying our strand bias test are absent as this software does not report forward and reverse strand counts.
The dictionary file, which is csv formatted, contains the word patterns with strand counts and verification status for all ROAs and reference sequences.
For TSS profiles, reads were aligned relative to RefSeq TSSs separated by strand, counted in 10 bp bins, inverted for negative strand genes, summed, smoothed over 4 windows on either side, and normalized by sequencing read count.
Application of the bi-directional coverage correction method II allowed us to determine the presence of 40 haplotypes, but such verification is laborious and raises concern regarding the acceptance of haplotypes characterized by high disproportion in forward and reverse strand counts.
Sequencing data at a single position in the genome can be represented by a 2 by 2 table c a d b where a, c represent the forward and reverse strands allele counts of the major allele, and b, d represent the forward and reverse strands' allele counts for the minor allele.
An average of 12.02±2.92 particles per strand (n = 47 strands) were counted in transverse arrays compared with 13.36±4.30 particles per strand (n = 47 strands) in longitudinal arrays (P>0.05, Wilcoxan Ranked Signed Test).
Ambiguous strands were counted as half reads for both strands.
Mutations on both strands were counted on the assumption that G-to-A transitions on the sequenced strand represent C-to-T transitions on the complementary strand.
