Release 3.1.3

This release introduces transcriptome assembly and quantification oriented versions of the annotation, removing alternative scaffolds as well as duplicated transcripts. CHM13 version of the annotation has tRNAs copied over from RefSeq.

Changelog

• Duplicated transcripts removed from .assembly.* files. Representative transcripts were chosen if 1. CDS matches MANE; 2. CDS is closest to MANE; 3. CDS maximizes Tukey's Median of the ILPIs of CDSs at each locus; 4. random choice
• tRNAs copied over to CHM13 version of CHESS from RefSeq

Statement

Chess Release 3.1.3

Files

Filenames	Genome	Content	Description
chess3.1.3.GRCh38.gff.gz, chess3.1.3.GRCh38.gtf.gz, chess3.1.3.GRCh38.bb.gz	GRCh38	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.
chess3.1.3.CHM13.gff.gz, chess3.1.3.CHM13.gtf.gz, chess3.1.3.CHM13.bb.gz	CHM13	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.
chess3.1.3.GRCh38.primary.gff.gz, chess3.1.3.GRCh38.primary.gtf.gz, chess3.1.3.GRCh38.primary.bb.gz	GRCh38	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.
chess3.1.3.GRCh38.assembly.gff.gz, chess3.1.3.GRCh38.assembly.gtf.gz, chess3.1.3.GRCh38.assembly.bb.gz	GRCh38	CHESS gene annotation excluding alternative scaffolds and duplicate transcripts	This file contains the assembly gene set described in the CHESS paper but excludes annotations of any alternative scaffolds and retains a single copy of each transcript duplicate. All genes and transcripts are mapped onto human genome release GRCh38.p12.
chess3.1.3.CHM13.assembly.gff.gz, chess3.1.3.CHM13.assembly.gtf.gz, chess3.1.3.CHM13.assembly.bb.gz	CHM13	CHESS gene annotation excluding alternative scaffolds and duplicate transcripts	This file contains the assembly gene set described in the CHESS paper but only retains a single copy of each transcript duplicate. All genes and transcripts are mapped onto the CHM13 human reference genome.
chess3.1.3.GRCh38.protein.fa.gz	GRCh38	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the GRCh38 human reference genome.
chess3.1.3.CHM13.protein.fa.gz	CHM13	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the CHM13 human reference genome.
chess3.1.3.mapfile.tsv	-	Cross-Reference	This tab-separated file contains a list of transcript identifiers in CHESS 3.1.0 along with the corresponding identifiers in other popular databases (RefSeq, GENCODE, CHESS2) .
assembled.gtf.gz	GRCh38	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

Release 3.1.2

This release addresses invalid new gene_id assignment for gene duplications identified by LiftOff on the CHM13 reference genome.

Changelog

1. Release 3.1.0 assigned gene_ids to gene duplications reported by LiftOff. An edge case resulted in multiple transcripts of the same duplication being assigned unique gene_ids. Those records were merged under the same gene_id this time.

Statement

Chess Release 3.1.2

Files

Filenames	Genome	Content	Description
chess3.1.2.GRCh38.gff.gz, chess3.1.2.GRCh38.gtf.gz, chess3.1.2.GRCh38.bb.gz	GRCh38	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.
chess3.1.2.CHM13.gff.gz, chess3.1.2.CHM13.gtf.gz, chess3.1.2.CHM13.bb.gz	CHM13	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.
chess3.1.2.GRCh38.primary.gff.gz, chess3.1.2.GRCh38.primary.gtf.gz	GRCh38	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.
chess3.1.2.GRCh38.protein.fa.gz	GRCh38	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the GRCh38 human reference genome.
chess3.1.2.CHM13.protein.fa.gz	CHM13	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the CHM13 human reference genome.
chess3.1.2.mapfile.tsv	-	Cross-Reference	This tab-separated file contains a list of transcript identifiers in CHESS 3.1.0 along with the corresponding identifiers in other popular databases (RefSeq, GENCODE, CHESS2) .
assembled.gtf.gz	GRCh38	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

Release 3.1.1

This release addresses an inconsistencies and incompleteness of the rRNA annotation specific to the CHM13 version of the CHESS annotation.

Changelog

1. rRNA annotation moved over from the official RefSeq CHM13 annotation, including all annotated copies
2. New gene and transcript IDs were assigned consistent with the CHS nomenclature
3. rRNA1 and rRNA2 genes on chrM assigned matching CHSID for GRCh38 and CHM13

Statement

Chess Release 3.1.1

Files

Filenames	Genome	Content	Description
chess3.1.1.GRCh38.gff.gz, chess3.1.1.GRCh38.gtf.gz, chess3.1.1.GRCh38.bb.gz	GRCh38	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.
chess3.1.1.CHM13.gff.gz, chess3.1.1.CHM13.gtf.gz, chess3.1.1.CHM13.bb.gz	CHM13	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.
chess3.1.1.GRCh38.primary.gff.gz, chess3.1.1.GRCh38.primary.gtf.gz	GRCh38	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.
chess3.1.1.GRCh38.protein.fa.gz	GRCh38	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the GRCh38 human reference genome.
chess3.1.1.CHM13.protein.fa.gz	CHM13	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the CHM13 human reference genome.
chess3.1.1.mapfile.tsv	-	Cross-Reference	This tab-separated file contains a list of transcript identifiers in CHESS 3.1.0 along with the corresponding identifiers in other popular databases (RefSeq, GENCODE, CHESS2) .
assembled.gtf.gz	GRCh38	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

Release 3.1.0

This release addresses several major and minor inconsistencies in the formatting of the CHESS annotation.

Changelog

1. Introducing gene features to the GFF3 files, full with RefSeq descriptors
2. All valid and complete ORFs now include the stop codon in the CDS coordinates. Some transcripts have been extended up to 3 positions to include the missing stop codon
3. Fixed duplicated gene IDs on the CHM13 version of the annotation. Gene copies identified by LiftOff are now assigned their own CHESS ID and the LiftOff metadata is stored in the auxiliary tags
4. Protein sequences based on the CHM13 genome sequence are now also included
5. Minor improvements to the comment lines

Statement

Chess Release 3.1.0

Files

Filenames	Genome	Content	Description
chess3.1.0.GRCh38.gff.gz, chess3.1.0.GRCh38.gtf.gz, chess3.1.0.GRCh38.bb.gz	GRCh38	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.
chess3.1.0.CHM13.gff.gz, chess3.1.0.CHM13.gtf.gz, chess3.1.0.CHM13.bb.gz	CHM13	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.
chess3.1.0.GRCh38.primary.gff.gz, chess3.1.0.GRCh38.primary.gtf.gz	GRCh38	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.
chess3.1.0.GRCh38.protein.fa.gz	GRCh38	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the GRCh38 human reference genome.
chess3.1.0.CHM13.protein.fa.gz	CHM13	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes based on the CHM13 human reference genome.
chess3.1.0.mapfile.tsv	-	Cross-Reference	This tab-separated file contains a list of transcript identifiers in CHESS 3.1.0 along with the corresponding identifiers in other popular databases (RefSeq, GENCODE, CHESS2) .
assembled.gtf.gz	GRCh38	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

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

CHESS 3.0

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

Changelog

1. Re-assembly and improved analysis of the dataset based on new methods described in a new paper.

Statement

Chess Release 3.0

Files

Filenames	Content	Description
chess3.0.gff.gz, chess3.0.gtf.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.CHM13.gff.gz, chess3.0.CHM13.gtf.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.primary.gff.gz, chess3.0.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.protein.fa.gz	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes.
chess3.0.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	4281	7204
alt_scaffolds	5258	10098

CHESS_v2.2

Changelog

1. Fixed wrong parent ids detected for several refseq transcripts
2. Added CDS annotations for novel isoforms in known protein-coding genes,which are start codon and intron-chain compatible with at least one known open reading frame from Gencode or Refseq
3. Fixed CDS coordinate overlaps
4. Re-added missing RefSeq CDS assignments
5. Re-added missing attributes from Gencode and Refseq

Statement

Chess Release 2.2

Files

Filename	Content	Description
chess2.2.gff.gz	CHESS gene annotation	This file contains the primary gene set described in the CHESS paper, in GFF format. All genes and transcripts are mapped onto human genome release GRCh38.p8. Included in this file are genes on the reference chromosomes, unmapped scaffolds, assembly patches, and alternate loci.
chess2.2.genes	CHESS gene list	This file is a table showing all 42,611 genes in CHESS release 2.2, in a tab-delimited text file with one gene per line. For each gene it provides features such as gene ID, type, gene name, source of the annotation, location(s), GFF ID(s), and a free text description of the gene.
chess2.2.protein.fa.gz	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes. For each gene locus that has more than one protein (e.g., splice variants), the longest protein sequence is provided.
chess2.2_assembly.gff.gz	Gene annotation for transcriptome assembly	This is a subset of the gene annotation GFF file (chess2.2.gff), containing annotations only on the reference chromosomes and the mitochondrion. It also includes the tRNA and rRNA gene annotations from RefSeq. We recommend using this file with transcriptome assemblers such as StringTie or Cufflinks.
chess2.2_and_refseq.gff.gz	CHESS plus RefSeq gene annotations	This is a superset of chess2.2.gff. It adds multiple other gene types annotated in Refseq that are not included in CHESS, such as pseudogenes, V_segements,C_segements,D_segements,J_segements, snoRNAs, snRNAs, telomerase RNAs, guide RNAs, etc. Note that many of these elements (e.g., pseudogenes) are not actually genes, but they are included here for users who want everything in RefSeq plus the additional genes in CHESS.

Summary

	genes	transcripts
protein_coding	20352	266331
lncRNA	18887	49892
other	3372	7035
total	42611	323258
novel_protein_coding	224	317
novel_lncRNAs	2671	3333

CHESS_v2.1

Statement

Chess Release 2.1

Files

Filename	Content	Description
chess2.1.gff.gz	CHESS gene annotation	This file contains the primary gene set described in the CHESS paper, in GFF format. All genes and transcripts are mapped onto human genome release GRCh38.p8. Included in this file are genes on the reference chromosomes, unmapped scaffolds, assembly patches, and alternate loci.
chess2.1.genes	CHESS gene list	This file is a table showing all 42,611 genes in CHESS release 2.1, in a tab-delimited text file with one gene per line. For each gene it provides features such as gene ID, type, gene name, source of the annotation, location(s), GFF ID(s), and a free text description of the gene.
chess2.1.protein.fa.gz	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes. For each gene locus that has more than one protein (e.g., splice variants), the longest protein sequence is provided.
chess2.1_assembly.gff.gz	Gene annotation for transcriptome assembly	This is a subset of the gene annotation GFF file (chess2.1.gff), containing annotations only on the reference chromosomes and the mitochondrion. It also includes the tRNA and rRNA gene annotations from RefSeq. We recommend using this file with transcriptome assemblers such as StringTie or Cufflinks.
chess2.1_and_refseq.gff.gz	CHESS plus RefSeq gene annotations	This is a superset of chess2.1.gff. It adds multiple other gene types annotated in Refseq that are not included in CHESS, such as pseudogenes, V_segements,C_segements,D_segements,J_segements, snoRNAs, snRNAs, telomerase RNAs, guide RNAs, etc. Note that many of these elements (e.g., pseudogenes) are not actually genes, but they are included here for users who want everything in RefSeq plus the additional genes in CHESS.

Summary

	genes	transcripts
protein_coding	20352	266331
lncRNA	18887	49892
other	3372	7035
total	42611	323258
novel_protein_coding	224	317
novel_lncRNAs	2671	3333

CHESS_v2.0

Statement

Chess Release 2.0

Files

Filename	Content	Description
chess2.0.gff.gz	CHESS gene annotation	This file contains the primary gene set described in the CHESS paper, in GFF format. All genes and transcripts are mapped onto human genome release GRCh38.p8. Included in this file are genes on the reference chromosomes, unmapped scaffolds, assembly patches, and alternate loci.
chess2.0.genes	CHESS gene list	This file is a table showing all 43,162 genes in CHESS release 2.0, in a tab-delimited text file with one gene per line. For each gene it provides features such as gene ID, type, gene name, source of the annotation, location(s), GFF ID(s), and a free text description of the gene.
chess2.0.protein.fa.gz	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes. For each gene locus that has more than one protein (e.g., splice variants), the longest protein sequence is provided.
chess2.0_assembly.gff.gz	Gene annotation for transcriptome assembly	This is a subset of the gene annotation GFF file (chess2.0.gff), containing annotations only on the reference chromosomes and the mitochondrion. It also includes the tRNA and rRNA gene annotations from RefSeq. We recommend using this file with transcriptome assemblers such as StringTie or Cufflinks.
chess2.0_and_refseq.gff.gz	CHESS plus RefSeq gene annotations	This is a superset of chess2.0.gff. It adds multiple other gene types annotated in Refseq that are not included in CHESS, such as pseudogenes, V_segements,C_segements,D_segements,J_segements, snoRNAs, snRNAs, telomerase RNAs, guide RNAs, etc. Note that many of these elements (e.g., pseudogenes) are not actually genes, but they are included here for users who want everything in RefSeq plus the additional genes in CHESS.

Summary

	genes	transcripts
protein_coding	21306	267478
lncRNA	18484	49314
other	3372	7035
total	43162	323827
novel_protein_coding	1178	1446
novel_lncRNAs	2268	2755

CHESS_v1.0

Statement

Initial release of CHESS human genome annotation

Files

Filename	Content	Description
chess1.0.gff.gz	CHESS gene annotation	This file contains the primary gene set described in the CHESS paper, in GFF format. All genes and transcripts are mapped onto human genome release GRCh38.p7. Included in this file are genes on the reference chromosomes, unmapped scaffolds, assembly patches, and alternate loci.
chess1.0.genes	CHESS gene list	This file is a table showing all 39,582 genes in CHESS release 1.0, in a tab-delimited text file with one gene per line. For each gene it provides features such as gene ID, type, gene name, source of the annotation, location(s), GFF ID(s), and a free text description of the gene.
chess1.0.protein.fa.gz	CHESS proteins	This FASTA file contains the sequences of all the proteins translated from the CHESS protein-coding genes. For each gene locus that has more than one protein (e.g., splice variants), the longest protein sequence is provided.
chess1.0_assembly.gff.gz	Gene annotation for transcriptome assembly	This is a subset of the gene annotation GFF file (chess1.0.gff), containing annotations only on the reference chromosomes and the mitochondrion. It also includes the tRNA and rRNA gene annotations from RefSeq. We recommend using this file with transcriptome assemblers such as StringTie or Cufflinks.
chess1.0_and_refseq.gff.gz	CHESS plus RefSeq gene annotations	This is a superset of chess1.0.gff. It adds multiple other gene types annotated in Refseq that are not included in CHESS, such as pseudogenes, V_segements,C_segements,D_segements,J_segements, snoRNAs, snRNAs, telomerase RNAs, guide RNAs, etc. Note that many of these elements (e.g., pseudogenes) are not actually genes, but they are included here for users who want everything in RefSeq plus the additional genes in CHESS.

Summary

	genes	transcripts
protein_coding	21635	304113
lncRNA	15985	41396
other	1962	6493
total	39582	352002
novel_protein_coding	1476	3543
novel_lncRNAs	1276	2256