NAME
create_Drop-seq_reference_metadata.sh - create Drop-seq reference metadata bundle
DESCRIPTION
USAGE: create_Drop-seq_reference_metadata.sh [options]
OPTIONS
-n <name> Name for reference metadata set to be created. Required.
- -r <referencefasta>
-
Reference fasta of the Drop-seq reference metadata bundle. Required.
- -s <species>
-
Species. Required.
- -g <gtf>
-
Gene annotation file. Required.
- -f <filtered-gene-biotype>
-
Annotations with the given gene_biotype will be filtered. Multiple values may be specified by using this argument more than once, and/or by providing a comma-separated list. Use ValidateReference command to see the gene_biotypes in your GTF in order to decide what to exclude. Default: not gene biotypes are filtered.
-d <dropseq_root> Directory containing Drop-seq executables. Default: directory containing this script.
- -o <outputdir>
-
Where to write output bam. Default: current directory.
- -t <tmpdir>
-
Where to write temporary files. Default: Value of 132153TMPDIR environment variable.
- -a <STAR_path>
-
Full path of STAR. Default: STAR is found via PATH environment variable.
- -b <bgzip_path>
-
Full path of bgzip: Default: bgzip is found via PATH environment variable.
- -i <samtools_path>
-
Full path of samtools. Default: samtools is found via PATH environment variable.
- -v
-
verbose
- -e
-
merely echo commands instead of executing