Usage

This section describes the general usage of HTSinfer.

General usage

htsinfer [--output-directory PATH]
         [--temporary-directory PATH]
         [--cleanup-regime {DEFAULT,KEEP_ALL,KEEP_NONE,KEEP_RESULTS}]
         [--records INT]
         [--threads INT]
         [--transcripts FASTA]
         [--read-layout-adapters PATH]
         [--read-layout-min-match-percentage FLOAT]
         [--read-layout-min-frequency-ratio FLOAT]
         [--library-source-min-match-percentage FLOAT]
         [--library-source-min-frequency-ratio FLOAT]
         [--library-type-max-distance INT]
         [--library-type-mates-cutoff FLOAT]
         [--read-orientation-min-mapped-reads INT]
         [--read-orientation-min-fraction FLOAT]
         [--tax-id INT]
         [--verbosity {DEBUG,INFO,WARN,ERROR,CRITICAL}]
         [-h] [--version]
         PATH [PATH]

The above command allows the user to infer metadata for single- or paired-ended RNA-Seq libraries by specifying file paths and relevant parameters. The tool outputs metadata in JSON format to STDOUT and logs to STDERR.

Command-line options

Available command-line parameters are categorized as follows:

General options

--output-directory	Path where output data will be saved.
--temporary-directory	Path for storing temporary files generated during execution.
--cleanup-regime	Specifies which data should be kept after completion. Options are: DEFAULT, KEEP_ALL, KEEP_NONE, KEEP_RESULTS
--verbosity	Controls the verbosity level of log output. Options are: DEBUG, INFO, WARN, ERROR, CRITICAL
-h, --help	Show help screen and exit.
-v, --version	Show version information and exit.

Processing and performance options

--records	Limits the number of input records to process; setting this to 0 will process all records.
--threads	Specifies the number of threads for STAR to optimize performance.
--tax-id	Taxonomy ID for the sample source, aiding in organism-specific analyses.

Library-specific options

PATH [PATH]	Path(s) to the RNA-Seq input data. For paired-end libraries, provide paths to both mate files.
--transcripts	Path to the FASTA file containing transcript sequences for reference.
--read-layout-adapters	Path to a file with 3’ adapter sequences (one sequence per line) used to identify adapter content.
--read-layout-min-match-percentage	Minimum percentage of reads containing an adapter for it to be considered as the library’s 3’-end adapter.
--read-layout-min-frequency-ratio	Minimum frequency ratio between the most and second most frequent adapters to select the 3’-end adapter.
--library-source-min-match-percentage	Minimum percentage of reads aligning with a library source for it to be considered representative of the library.
--library-source-min-frequency-ratio	Minimum frequency ratio between primary and secondary library sources, ensuring only the most prominent source is identified.
--library-type-max-distance	Maximum allowable distance between read pairs to classify the library type.
--library-type-mates-cutoff	Ratio cutoff to determine the consistency of mate orientation in paired-end reads.
--read-orientation-min-mapped-reads	Minimum number of mapped reads to ensure reliable inference of read orientation.
--read-orientation-min-fraction	Minimum fraction (must exceed 0.5) of reads supporting a given orientation to confirm its accuracy.