Skip to content

Release 3.1.3

Latest
Latest
Compare
Choose a tag to compare
@alevar alevar released this 31 Jul 16:02
· 1 commit to master since this release
v.3.1.3
5bd459e

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
Assets 21
Loading