GRCh38

STAR index (GRCh38)

Pitagora-CWL reference data for testing

Used in

• star-cufflinks
• star-stringtie

Data availability

• location
  • Amazon S3
    • https://s3.amazonaws.com/nig-reference/GRCh38/star_index/star_GRCh38.tar.gz
  • Zenodo
    • https://zenodo.org/record/2587202/files/star_GRCh38.tar.gz?download=1
• file size: 23.1GB
• md5: 3e185ac85ea5aa32550d455554f72453

How to create

1. Download GRCh38 reference genome fasta file from UCSC Genome browser FTP site.
2. Download Comprehensive gene annotation GTF format file in Gencode Human Release 28 (GRCh38.p12) from Gencode FTP server.
3. gunzip to unarchive genome fasta and annotation gtf.
4. Run STAR --runMode genomeGenerate with the docker container quay.io/biocontainers/star:2.6.0c--0 and star_index.cwl with default parameters as specified in the CWL definition (--sjdbOverhang 100) giving reference genome fasta to genomeFastaFiles and annotation gtf to sjdbGTFfile.