Drop-seq_alignment.sh1
Perform drop-seq tagging, trimming and alignment
Overview
USAGE: Drop-seq_alignment.sh [options] <unmapped-queryname-sorted.bam>
Options
-g <genomedir> Directory of STAR genome directory. Required.
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-r <referencefasta> -
Reference fasta of the Drop-seq reference metadata bundle. Required.
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-d <dropseq_root> -
Directory containing Drop-seq executables. Default: directory containing this script.
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-o <outputdir> -
Where to write output bam. Default: current directory.
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-t <tmpdir> -
Where to write temporary files. Default: a new subdirectory in .
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-s <STAR_path> -
Full path of STAR. Default: STAR is found via PATH environment variable.
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-e -
Echo commands instead of executing them.
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-k -
Keep intermediate files
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).