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Contents

The detailed information on each file is given below.

Projection classification metadata

• projection_features.tsv
• trans_to_chain_classes.tsv

Preprocessing metadata

• fragmented_projections.tsv
• memory_requirements.tsv
• paralogous_projections_to_align.tsv
• processed_pseudogene_projections_to_align.tsv
• spanning_chain_ref_coords.tsv

Extended data

• loss_summary_extended.tsv
• query_annotation.with_discarded_exons.bed

Alignment step metadata

• exon_meta.tsv.gz
• selenocysteine_codons.tsv
• transcript_meta.tsv.gz

Splice site and SpliceAI correction metadata

• gained_intron_summary.tsv
• splice_site_shifts.tsv
• splice_sites.tsv.gz

Gene tree-based orthology resolution meta

• gene_tree_job_summary.tsv
• resolved_tree_pairs.tsv
• one2zero_genes.txt
• unresolved_tree_clades.txt

Rejected projection files

• discarded_projections.bed
• discarded_overextended_projections.txt
• rejected_at_orthology_step.tsv
• redundant_paralogs.txt
• redundant_processed_pseudogenes.txt