The following layer, Checkpoint and Replication, provides a checkpointing mechanism, through the use of virtual machines (VMs), and provides several options for partitioning and replicating input data.
To estimate false discovery rates, this analysis was performed on replicate total input fractions in which the log2(Total Input replicate1/Total Input replicate2) was used in place of log2(M/T).
Differentially expressed genes were identified using the feature-assigned fragment counts for each replicate as input to the DESeq software [ 32].
In this equation, ROR ¯ Nj is the average of two replicates at the nominal level and ROR ¯ Lj s the average of two replicates for input levels within specification, or is the single result for input levels outside of specification.
In its function as a fault-tolerance and data management system, as the user provides data to the framework, the HDFS splits and replicates the input data across a number of cluster nodes.
For all replicates of Input and H3 and H3K36me3 ChIP experiments, the read count per base pair was scaled so that the median read count across the genome was the same.
Two biological ChIP-seq replicates and inputs were collected for AML1, AML1-ETO, p300, N-CoR, H3K4me3, and H3K27me3.
