Provided by: drop-seq-tools_2.5.3+dfsg-1_all
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
SEE ALSO
Drop-seq_alignment.sh(1)