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Figure 2 | BMC Genomics

Figure 2

From: Systematic characterization of small RNAome during zebrafish early developmental stages

Figure 2

The computational pipeline in CSZ. First, total reads were mapped to reference genome, while mapped reads were successively mapped to miRBase, Rfam, repeat annotations, RefSeq mRNAs, and piRNABank to identify miRNAs, ncRNAs (including rRNA, tRNA, and snRNA/snoRNA), repeats, mRNAs and piRNAs. Based on the annotation information for genomic repeats, the ncRNAs were recalled and repeat-associated piRNAs were characterized from remaining repetitive sequences. For the unclassified reads, MIREAP and miRDeep2 were used for the prediction of novel miRNAs, which were further validated by ZmirP to reduce potentially false positive hits.

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