chess-genome/chess: 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

1. 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
2. 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 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.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 |