cov2Vero ref genome with STAR index
Combines, in this order
- SARS-CoV-2 strain WuHan-1 NC_045512.2
- Hg38 (Human GRCh38/seqs_for_alignemtn_piplines.ucsc_ids)
and then indexes the combined genome with STAR (overhang=100), BWA,
For use with the CCTS-Informatics-Pipelines/Snakemake-Eukaryotic-RNAseq-Pipeline
Edit config.yaml of the Snakemake-Eukaryotic-RNAseq-Pipeline to set
# required for RNA-Seq analysis
index: "/data/project/public_datasets/ngs/genomes/cov2WuHan1_hg38/cov2WuHan1_hg38noAlt/STAR/STAR_2.5.3a-100"
annotation: "/data/project/public_datasets/ngs/genomes/cov2WuHan1_hg38/cov2WuHan1_hg38noAlt/cov2WuHan1_hg38noAlt.gtf"
# optional - for bwa alignment
bwa: "/data/project/public_datasets/ngs/genomes/cov2WuHan1_hg38/BWA/0.7.13/cov2WuHan1_hg38noAlt.fa"
# optional - for creating sample-specific genomes
cov2: "/data/project/public_datasets/ngs/genomes/cov2WuHan1_hg38/cov2WuHan1/NC_045512.2.fasta"