tRNA Analysis¶
The tRNA Analysis module provides precise quantification and modified coverage assessment for tRNA species.
Overview¶
tRNA genes are densely modified and highly repetitive, requiring specialized alignment strategies to avoid mapping biases.
Workflow¶
graph LR
A[Trimmed FASTQ] --> B[mim-tRNA-seq]
B --> C[tRNA Quantification]
C --> D[tRNA Analysis Results]tRNA Quantification¶
The pipeline implements the mim-tRNA-seq strategy for quantifying tRNA abundance.
Features¶
- Optimized for heavily modified tRNA sequences.
- Dynamic alignment parameters.
- Comprehensive annotation from GtRNAdb.
tRNA Annotation¶
The pipeline uses annotations from GtRNAdb, which are highly curated and provide detailed information on tRNA isoacceptors and isodecoders.
Parameters & Defaults¶
| Parameter | Default | Description |
|---|---|---|
method |
standard |
Choice between standard and mim-tRNA-seq. |
mimseq_params.max_mismatches |
2 |
Max mismatches for mim-tRNA-seq alignment. |
mimseq_params.cluster_identity |
0.8 |
Identity threshold for clustering tRNAs. |
Results¶
| Location | Description |
|---|---|
results/tRNA_coverage/ |
tRNA coverage maps and quantification results. |
results/analysis/rdata/ |
Normalized tRNA counts for downstream analysis. |
results/analysis/tables/ |
tRNA-specific quantification tables. |
results/references/gtrnadb/ |
Down-loaded tRNA annotations. |