A template-based Bayesian method for identifying nucleosome positions at base-pair resolution
For each experiment, 0.5 µg of mono-nucleosomal DNA (~5 pmol) was used for sequencing library construction according to the Illumina Truseq paired-end protocol.  ~1 pmol of paired-end ligated library was recovered from the agarose gel for each experiment before PCR amplification.  Since the amount of ligated library is sufficient for sequencing, we only performed 4 cycles of PCR amplification with the Illumina primer cocktail to obtain a double strand sequencing library.  The number of sequencing clusters generated on the flow-cell represented at most 1/10,000 of the amplified library, such that the chance is very small to have more than one copy of duplicated library molecules clustered on the flow-cell (p<1.8×10-5, binomial distribution).  Therefore we treated each paired-end read as an individual nucleosome from a single cell.  Libraries were sequenced with an Illumina Hiseq 2000 and the paired-end sequencing reads were aligned to the S. cerevisiae genome Scer02 with bowtie 2.0 (Langmead et al., 2009).  We mapped reads with two or fewer mismatches, and insert lengths were restricted to between 100 bp and 300 bp.  Reads with multiple reportable alignments were randomly assigned to one such alignment.  The midpoints of all sequenced DNA fragments were randomly rounded to an integer genomic coordinate and used to generate sequencing read midpoint occupancy maps.