Statistical analysis and Quality Control
Basic Analysis
Counts, Ratio and Length of different RNA type
- Ratio Pie Plot
Count the proportion of different RNA type and show them in a pie chart
- Ratio Box Plot
Count the proportion of different RNA type and show them in a boxplot
Count the proportion of different RNA type and show them by sample
- 3D bar plot
- Stack Bar ratio plot
- Stack Bar count plot
- Length Line Plot
Counting the length distribution of mapped reads of different RNA types
- Length 3D Bar Plot
Counts of specific RNA types in different samples
- Bar plot of ratio
- Bar plot of count
Sample QC
We have developed a set of criteria for quality control of samples based on the ratio of different RNA type reads:
| Check point | Threshold | Notes |
|---|---|---|
| Raw reads quality | reads quality >28 (median lines in green area) | Check fastqc results(*.html) |
| Clean reads number | > 10 million | Adaptors and too-short sequences removed reads |
| rRNAs% | < 10% | Reads mapped to rRNAs (all following % are divided by the total number of clean reads) |
| HG% | > 60% (optional) | Reads mapped to Human Genome except rRNAs |
| Transcriptome% | > 50% | Reads mapped to Human Transcriptome (including rRNA, miRNA, piRNA, Y RNA, srpRNA, snRNA, snoRNA, tRNA, mRNA exons, lncRNA exons, TUCP exons) |
| Y RNA% | 10%~65% | Reads mapped to Y RNA |
| miRNA% | 10%~65% (up to 80% for exoRNAs) | Reads mapped to miRNA |
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FastQC
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Sample QC
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[ ] to do: sample QC