Table 1.
SQANTI-reads-specific output files
| Output file | Description | Default output | Output type |
|---|---|---|---|
| gene_counts.csv | Number of reads in each structural category, per gene, and per sample | Yes | Multiple samples file |
| ujc_counts.csv | List of junction hashes in each sample and the number of reads in each sample associated with each junction string. Flags the most expressed UJC per gene | Yes | Multiple samples file |
| length_summary.csv | Number and percentage of reads in length categories per sample | Yes | Multiple samples file |
| cv.csv | Metrics on the coefficient of variance of reference junctions for each sample | Yes | Multiple samples file |
| jxn_counts.csv | Number of known canonical, novel canonical, known noncanonical, and novel noncanonical junctions in reads of each sample | - - all-tables | Multiple samples file |
| cv_acc_counts.csv cv_don_counts.csv |
Number of detected annotated donors and acceptors in each junction variation category | - - all-tables | Multiple samples file |
| FSM_counts.csv ISM_counts.csv NIC_NNC_counts.csv |
Number of reads in each subcategory for FSMs, ISMs, NICs, and NNCs | - - all-tables | Multiple samples file |
| err_counts.csv | Number and percentage of reads with evidence of intrapriming, RT-switching, and noncanonical junctions per sample | - - all-tables | Multiple samples file |
| pca_loadings.csv | PC1 and PC2 loadings from PCA | - - pca-tables | Summary file |
| pca_variance.csv | Variance explained by each PC | - - pca-tables | Summary file |
| sample_quality_flags.csv | Binary quality indicators to flag potential sample issues | Yes | Summary File |
| gene_classification.csv | For genes with coverage over a user-defined threshold, gives the annotation category of each gene | Yes | Summary file |
| putative_underannotation.csv | Metrics on NIC and NNC UJCs and flags putative novel transcripts | Yes | Summary file |
