Figure 2.
Data analysis protocols of the secondary stage. (A) The secondary stage is critical for NGS-based projects. Four different types of data analysis protocols are summarized here. Each of them serves their corresponding investigation purposes and goals. However, they share common procedures that are the read quality control and read mapping: Cufflinks,188 EdgeR,189 DEGseq,190 MACS,191 cisGenome,192 PeakSeq,193 SISSr,194 bismark,195 BS-seeker,196 BSMAP,197 methyKit,198 MAQ,74 bam2 mpg,76 GATK,78 and Samtools.77 (B) Sequence alignment, SNV detection, and SV detection are major parts for the secondary stage of workflow, whose results determine the quality of the downstream analysis in the NGS workflow.