CHESS 3.0.1

First release of the upcoming new major version of the CHESS annotation.

Changelog

1. Updated simplified source values
2. Gene records in GTF/GFF
3. BED14 files
4. TPM and sample count attributes simplified and made consistent for all assembled transcripts
5. Proper comment appended
6. 24 Erroneous pseudogene transcripts removed

Statement

Chess Release 3.0.1

Files

Filenames	Content	Description
chess3.0.1.gff.gz, chess3.0.1.gtf.gz, chess3.0.1.bb.gz	CHESS gene annotation	This file contains the primary gene set described in the CHESS paper. All genes and transcripts are mapped onto human genome release GRCh38.p12. Included in this file are genes on the reference chromosomes, unmapped scaffolds, assembly patches, and alternate loci.
chess3.0.1.CHM13.gff.gz, chess3.0.1.CHM13.gtf.gz, chess3.0.1.CHM13.bb.gz	CHESS gene annotation on CHM13	This file contains the primary gene set described in the CHESS paper mapped over to the CHM13 human reference genome.
chess3.0.1.primary.gff.gz, chess3.0.1.primary.gtf.gz	CHESS gene annotation excluding alternative scaffolds	This file contains the primary gene set described in the CHESS paper but excludes annotations of any alternative scaffolds. All genes and transcripts are mapped onto human genome release GRCh38.p12.
chess3.0.1.protein.fa.gz	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes.
chess3.0.1.mapfile.tsv	Cross-Reference	This tab-separated file contains a list of transcript identifiers in CHESS 3.0 along with the corresponding identifiers in other popular databases (RefSeq, GENCODE, CHESS2) .
assembled.gtf.gz	Assembled Transcripts	Noise-filtered set of assembled GTEx transcripts used to generate the final CHESS dataset.

Summary

	genes	transcripts
protein_coding	19838	99201
lncRNA	17624	34709
pseudogene	16774	17263
other	4269	7190
alt_scaffolds	5250	10088