exom sequencing workflow for use with qproject.
TODO: Adapt readme to exomseq.
Add a config file "params.json" in etc:
{
"gtf": "path/to/gtf",
"indexed_genome": "path/to/genome/basename",
"stranded": "yes",
"overlap_mode": "union",
"feature_type": "exon",
"gff_attribute": "gene_id",
"normalize_counts": "deseq2"
}where indexed_genome and gtf are paths relative to ref.
indexed_genome is the basename of a bowtie2 index.
The parameters stranded, overlap_mode, feature_type and gff_attribute
are explained in the htseq documentation.