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Fig. 1 | BMC Genomics

Fig. 1

From: Novel microRNA discovery using small RNA sequencing in post-mortem human brain

Fig. 1

Flowchart depiction of the novel miRNA discovery pipeline. This flowchart shows our novel miRNA discovery pipeline beginning with the small RNA sequencing of tissue samples, quality control (cutadapt v. 1.2.1, FASTX-Toolkit v. 0.0.14) and alignment of sequencing reads in fastq file format, and preparation of alignment (bam) files for miRDeep*. The miRNA predictions made by miRDeep* were classified as false positives (gencode v19 exons/sRNA), true positives (miRBase v20 miRNA), or potential novel miRNAs, which were filtered further. In the flowchart, the yellow box represents miRDeep* results that occurred on both exon and miRNA annotations, which were excluded from the analysis. The false positives were used to determine a miRDeep* score threshold with a false positive rate close to 0.05, which was used to filter the miRDeep* results that are neither false positives nor true positives. The result of this filtering step was a final set of putative novel miRNAs. This set was annotated with differential expression analysis (HD/C and PD/C), alignment (SSEARCH) of mature miRNA sequences to known human mature miRNA sequences in miRBase v20, and proximity to human genes

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