High quality reads ranging from 450 bp to 850 bp in length were clustered into OTUs at 97% sequence similarity.
Trimmed sequences >100 bp in length were clustered into putative unique gene objects (unigenes).
Chimeras were detected and removed with the program UCHIME [ 61], high quality reads greater than 700 bp in length were clustered into OTUs at 97% similarity; rarefaction curves, richness estimates, and other indices of ecological diversity were computed using Mothur [ 62].
Then, the selected TSSs were clustered into 500 bp bins (iTSCs) in every cell type.
For the TSS Seq analysis, the TSS tags were clustered into 500-bp bins.
Reads less than 500 bp apart and on the same strand were clustered into peaks containing a minimum of a single read and annotated using the RepeatMasker track from human genome build hg19 and locations of known non-reference elements.
The 104928 reads were clustered into 2664 contigs and 50,531 singletons with an average length of 508 bp and 231 bp, respectively, for the expression analysis (Table 1a).
According to a recent study, the cNA are present in the circulation at sizes lower than 1200 bp and most of cNA molecules are clustered into two peaks, first at approximately 162 bp and second at 340 bp, representing a dominant and a minor peak [ 1].
EST sequences longer than 100 bp after trimming were clustered and assembled into contigs and singletons (unisequences) via EST Clustering, which was designed based on the MegaBlast and CAP3 programs (Huang and Madan, [ 34]; Zhang et al., [ 35]).
For example, 200-bp reads are clustered at 99.0% identity, so that small clusters are recruited into their primary clusters.
