A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/Users/jonathan.manning/projects/MultiQC/ribotish_plugin/Chen_2020
General Statistics
| Sample Name | Weighted F0 % | % in 28-30nt | Best F0 % | Best F0 Length (nt) | Peak Length (nt) | Length Range (nt) | Total Reads |
|---|---|---|---|---|---|---|---|
| SRR9113062_GSM3791723_iPSC_harringtonine-treated_Homo_sapiens_qual | 64.0% | 47.5% | 74.3% | 28 | 30 | 25-34 | 20755546 |
| SRR9113063_GSM3791724_Cardiomyocyte_harringtonine-treated_Homo_sapiens_qual | 72.8% | 68.5% | 80.7% | 28 | 29 | 25-34 | 8067784 |
| SRR9113064_GSM3791725_iPSC_no_drug_treatment_replicate_1_Homo_sapiens_qual | 74.7% | 70.5% | 81.7% | 30 | 30 | 25-34 | 15012625 |
| SRR9113065_GSM3791726_iPSC_no_drug_treatment_replicate_2_Homo_sapiens_qual | 73.6% | 69.3% | 82.1% | 28 | 30 | 25-34 | 12387378 |
| SRR9113066_GSM3791727_iPSC_no_drug_treatment_replicate_3_Homo_sapiens_qual | 73.9% | 70.0% | 82.6% | 28 | 30 | 25-34 | 11301689 |
| SRR9113067_GSM3791728_Cardiomyocyte_no_drug_treatment_replicate_1_Homo_sapiens_qual | 68.1% | 64.1% | 76.7% | 28 | 29 | 25-34 | 2078698 |
| SRR9113068_GSM3791729_Cardiomyocyte_no_drug_treatment_replicate_2_Homo_sapiens_qual | 72.5% | 68.1% | 81.7% | 28 | 29 | 25-34 | 4201556 |
| SRR9113069_GSM3791730_Cardiomyocyte_no_drug_treatment_replicate_3_Homo_sapiens_qual | 74.2% | 70.3% | 82.9% | 28 | 29 | 25-34 | 4597558 |
Ribo-TISH
Identifies translated ORFs from Ribo-seq data and reports reading frame quality metrics.https://github.com/zhpn1024/ribotishDOI: 10.1186/s13059-017-1316-1
Reading Frame Proportions
Proportion of reads in each reading frame (Frame 0, 1, 2) for different read lengths (25-34nt). Frame assignment is based on P-site positions as determined by Ribo-TISH. Some degree of frame preference (enrichment in Frame 0) is typically expected in Ribo-seq data.
This plot shows the distribution of reads across the three reading frames for each read length, based on P-site positions.
- Frame 0: The primary reading frame
- Frame 1: Offset by 1 nucleotide from Frame 0
- Frame 2: Offset by 2 nucleotides from Frame 0
Ribo-seq data typically shows enrichment in Frame 0, particularly for read lengths 28-30nt, though the degree of frame preference can vary depending on the experimental protocol (e.g., RNase I vs. MNase treatment).
Red dashed reference lines mark the expected proportions (33.3% and 66.7%) if reads were randomly distributed across frames. Good quality Ribo-seq data should show Frame 0 proportions well above the 33.3% threshold.
Read lengths are shown as separate bars for each sample.
Read Length Distribution
Percentage of reads at each read length for each sample. Ribo-seq data typically shows enrichment around 28-30nt, representing ribosome-protected fragments.
This plot shows what percentage of total reads each read length represents for each sample.
- Each line represents a different sample
- Peaks indicate the most common read lengths
- Multiple samples can be easily compared
The expected read length distribution can vary depending on the experimental protocol and organism.
Read Length Distribution (Heatmap)
Alternative heatmap view of read length distribution. Useful for comparing many samples at once.
This heatmap shows what percentage of total reads each read length represents for each sample.
- Rows are samples, columns are read lengths
- Darker blue indicates higher percentage of reads
- Lighter colors indicate fewer reads
This view is particularly useful when comparing many samples simultaneously.