CATS-rf

Output explanation

Summary table

Summary files represent the main output of CATS-rf. In paired-end mode, four summary files are produced:

assembly_score_summary.tsv contains descriptive statistics of transcript score components and the overall assembly score. The content of this file is printed when CATS-rf finishes running in paired-end mode.

general_statistics_table.tsv contains descriptive statistics of transcript length (mean, median, interquartile range, range, N50, L50, N90, L90), GC content, and read mapping rate.

coverage_and_accuracy_analysis_summary.tsv contains summarized results of coverage and accuracy analysis. The content of this file is printed when CATS-rf finishes running in single-end mode.

paired_end_read_analysis_summary.tsv contains summarized results of paired-end read analysis, including local fidelity and integrity analysis.

CATS-rf also produces several .tsv files containing detailed per-transcript metrics:

Transcript score components

transcript_scores.tsv contains CATS-rf score components and transcript score for each transcript.

Coverage analysis

coverage_stats.tsv contains coverage analysis results for each transcript:

Column	Description
transcript	Transcript name
covered_base_N	Number of covered bases
covered_base_prop	Proportion of covered bases
covered_base_prop_category	Proportion of covered bases category
coverage_mean	Mean transcript coverage
coverage_mean_category	Mean transcript coverage category
uncov_region_length_max	Maximum uncovered region length
transcript_end_coverage_mean	Mean transcript end coverage
lcr_base_N	Number of bases in low-coverage regions
lcr_base_prop	Proportion of bases in low-coverage regions
lcr_base_prop_category	Proportion of bases in low-coverage regions category
coverage_score_component	Coverage score component

per_base_coverage_distribution.tsv contains distribution of assembly-level per-base coverage.

relative_coverage_median_by_transcript_position.tsv contains median values of mean relative coverage per transcript fraction.

lcr_list.tsv contains low-coverage region coordinates.

Accuracy analysis

accuracy_stats.tsv contains accuracy analysis results for each transcript:

Column	Description
transcript	Transcript name
acc_base_N	Number of accurate bases
acc_base_prop	Proportion of accurate bases
acc_base_prop_category	Proportion of accurate bases category
lar_base_N	Number of bases in low-accuracy regions
lar_base_prop	Proportion of bases in low-accuracy regions
lar_base_prop_category	Proportion of bases in low-accuracy regions category
accuracy_score_component	Accuracy score component

per_base_accuracy_distribution.tsv contains distribution of assembly-level per-base accuracy.

accuracy_median_by_transcript_position.tsv contains median values of mean accuracy per transcript fraction.

lar_list.tsv contains low-accuracy region coordinates.

Local fidelity analysis

local_fidelity_stats.tsv contains local fidelity analysis results for each transcript:

Column	Description
transcript	Transcript name
unmapped_pair_read_N	Number of reads with pair not mapped to the assembly
unmapped_pair_read_prop	Proportion of reads with pair not mapped to the assembly
unmapped_pair_tr_end_read_N	Number of reads with pair not mapped to the assembly on transcript ends
unmapped_pair_tr_end_read_prop	Proportion of reads with pair not mapped to the assembly on transcript ends
improp_pair_orientation_read_N	Number of reads with pair mapped in an unexpected orientation
improp_pair_orientation_read_prop	Proportion of reads with pair mapped in an unexpected orientation
improp_pair_distance_read_N	Number of reads with pair mapped too far apart
transcript_distance_penalty	Transcript distance penalty
improp_pair_within_tr_read_N	Number of improperly paired reads within a transcript
improp_pair_within_tr_read_prop	Proportion of improperly paired reads within a transcript
improp_pair_within_tr_read_prop_category	Proportion of improperly paired reads within a transcript category
local_fidelity_score_component	Local fidelity score component

read_pairs_mapping_in_unexpected_orientation.tsv contains coordinates of read pairs mapping in an unexpected orientation.

read_pairs_mapping_too_far_apart.tsv contains coordinates of read pairs mapping too far apart.

Integrity analysis

integrity_stats.tsv contains integrity analysis results for each transcript:

Column	Description
transcript	Transcript name
pair_mapped_to_other_tr_N	Number of reads with pair mapped to another transcript
pair_mapped_to_other_tr_prop	Proportion of reads with pair mapped to another transcript
pair_mapped_to_other_tr_prop_category	Proportion of reads with pair mapped to another transcript category
bridge_N	Number of reads representing bridging events
bridge_prop	Proportion of reads representing bridging events on transcript ends
integrity_score_component	Integrity score component

read_pairs_mapping_to_different_transcripts.tsv contains coordinates of read pairs mapping to different transcripts.

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