For secondary analyses involving an independent set of SNPs, we used PLINK to prune the genotype data in windows of 50 bp (base pairs), removing one SNP from each pair of SNPs with r > 0.05.
In this article, we present Pindel, a method that uses pattern growth algorithm to identify the break points of large deletions (1 bp–10 kb) and medium sized insertions (1 20 bp) from 36 bp paired-end short reads.
We cloned three PCR fragments (308 bp, 481 bp, and 1013 bp) derived from the Tel/34R primer pair and one PCR fragment (940 bp) from the Tel/14R primer pair.
Given we have pair-end reads of length 50 bp from adipose tissue, we treated each pair as two single-end reads and mapped each one independently.
Clonal coverage can be defined as the genomic coverage (that is, 30×) multiplied by the length of the insert (1,500 bp), divided by the amount of sequence derived from each mate pair (100 bp).
Library construction of digital gene expression sequencing (DGE; BGI-Shenzhen, China) generates tags with 21 base pairs (bp) from the 3' ends of each transcript, and such tags are utilized to represent the expression levels of transcripts [ 12].
About 40 bp oligonucleotides from base pairs 165-205 were synthesized as sense and antisense (GeneSet oligos) and used as probes.
The linear regression line between mean telomere length (measured by terminal restriction fragment analysis based on Southern blotting) and the T/S ratio (measured by the quantitative PCR based method) was obtained, as described previously (14, 16), and used for the calculation of the corresponding telomere length in base pairs (bp) from the T/S ratio measured in each subject.
To ensure complete coverage of each exon, primers were at least 50 base pairs (bp) from the intron-exon boundary.
GIS analysis is a SAGE modification which isolates tags of 18 base pairs (bp) from the 5'- and 3'-ends of a transcript and concatenates them to form Paired-End diTag (PET) structures.
