GRCh38

Gencode annotation data (GRCh38, v28)

Pitagora-CWL reference data for testing

Used in

• tophat2-cufflinks
• hisat2-cufflinks
• hisat2-stringtie
• star-cufflinks
• star-stringtie

Data availability

• location
  • Amazon S3
    • https://s3.amazonaws.com/nig-reference/GRCh38/gencode_v28_annotation/gencode.v28.annotation.gtf.gz
  • Zenodo
    • https://zenodo.org/record/2587202/files/gencode.v28.annotation.gtf.gz?download=1
• file size: 37MB
• md5: 0c64fd0ab90aef446119d113ca62252f

How to create

1. Download the Comprehensive gene annotation GTF format file in Gencode Human Release 28 (GRCh38.p12) from the Gencode FTP server.
2. gunzip to unarchive.

It contains the comprehensive gene annotation on the reference chromosomes only This is the main annotation file for most users