Table 1.
Workflow summary
| LoadExp+ Workflow | Analysis Tool(s) | Detailed Workflow Information (CoGe Wiki) | Visualization (Browser Track) | Analysis |
|---|---|---|---|---|
| RNA‐seq | Cufflinks (Trapnell et al., 2010) | https://goo.gl/KCBtbH | Alignment, Read Depth (bar plot), FPKM (bar plot) | FPKM Differential expression |
| Bisulfite‐seq |
Bismark (Krueger & Andrews, 2011) BWAmeth (Pedersen, Eyring, De, Yang, & Schwartz, 2014) |
https://goo.gl/2eegqK | Alignment, Percent Methylation (bar plot) | Whole‐genome DNA methylation |
| ChIP‐seq | HOMER (Heinz et al., 2010) | https://goo.gl/aFV2T5 | Peaks (bar plot) | Protein–DNA Interactions |
| Variant calling | SAMtools (Li et al., 2009), Platypus (Rimmer et al., 2014), GATK (McKenna et al., 2010), CoGe Basic | https://goo.gl/GlQGu5 | SNP Genome Browser Track | SNP Discovery |
| Population Genetics | Nucleotide diversity, Watterson's estimator, and Tajima's D | https://goo.gl/j4nNS1 | Custom report | Identification of selection, selective sweeps |