For all three datasets, NEXT-peak had the smallest mean distances among all programs; it had one of the smallest biases as well.
Long regions with small p-values suggest multiple binding sites, so for all datasets NEXT-peak masked regions less than a certain length long and with small p-values.
For the St . Louisdataset, next-generation sequencing reads were aligned to hg19 human reference sequence and variants were called and annotated, as described by Buchan et al. (2014).
After determining the quality of the Kaiso ChIP-seq datasets, the next step was to select a defined peak set for further analysis.
The curated sequence datasets were next clustered using PCAP software [ 19] with parameters of 95% overlap identity and 60 bp overlap length [ 17].
After determining that, indeed, FAIME-derived mechanisms improve overlap among different independent datasets, we next explored whether these FAIME-derived mechanisms overlapped amongst themselves.
These parameters are similar to those reported for previously sequenced genomes using the same technology (e.g. [ 20, 21, 34]) and other human datasets using next generation sequencing (Additional file 2).
Having identified genotype as the main factor determining transcriptional variation in our 6 datasets, we next set out to determine a gene set that showed high confidence expression differences between C600 and Roberta genotypes.
