create_Drop-seq_reference_metadata.sh - create Drop-seq reference metadata
bundle
USAGE: create_Drop-seq_reference_metadata.sh [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
Drop-seq_alignment.sh(1)