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Fig. 5 | Genome Biology

Fig. 5

From: miRTrace reveals the organismal origins of microRNA sequencing data

Fig. 5

miRTrace quality control report. a Sequencing quality. Higher Phred scores indicate higher sequencing quality. In this case, all samples pass the filter. The number above each column shows the number of sequences in the dataset. b Length of sequenced transcripts. miRNAs are ~ 22 nucleotides long, while the fly 2S RNAs are ~ 30 nucleotides long. Zero-length sequences indicate adapter artifacts, while lengths of > 50 indicate that the sequencing adapter has not been successfully identified. Four samples are flagged because < 25% of the sequences are between 20 and 25 nucleotides long. c Quality control. After the ligation adapter has been removed, sequences are grouped according to length and sequencing quality. The most desirable sequences have the adapter removed and are long enough to map reliably (18 nucleotides or longer). d RNA type. For most applications, a high miRNA content and low rRNA and tRNA content are desirable. Illumina sequences are tagged as “artifacts.” Here, three samples are flagged because the miRNA content is < 10%. e miRNA sequence complexity. Each bar shows the number of distinct miRNA sequences as a function of sequencing depth. Two samples are flagged because < 10% of all known miRNAs for the studied species (human) is represented in the sample. f Contamination. The human samples that are intentionally contaminated with fly clearly stand out (in beige color). In total, 14 clades are considered, but here only eight are shown in the table below. Samples: Fly control, S2 cells; Human/Fly 10:1, total RNA from HEK-293T cells mixed with total RNA from S2 cells in ratio 10:1; Human control, HEK-293T cells; Low-input RNA, 50 ng total RNA from HEK-293T cells; Degraded RNA, HEK-293T total RNA incubated with RNase A enzyme; Incorrect adapter, wrong adapter sequence designated when starting the analysis. The six report figures here are imported directly from miRTrace output, except for the small gray arrows and the accompanying annotations, which have been added here for clarification

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