Markup | Genome Research

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