kallisto
Quantify abundances of transcripts from bulk and single-cell RNA-Seq data.
$ pbrun kallisto \
--ref Homo_sapiens_assembly38.fasta \
--in-fq input1.fastq \
--index /path/to/kallisto/index \
--index-out output_index_file \
--output-dir output_directory
Quantify abundances of transcripts from bulk and single-cell RNA-Seq data.
Input/Output file options
- --index INDEX
- --ref REF
- --index-out INDEX_OUT
- --in-fq [IN_FQ [IN_FQ ...]]
- --output-dir OUTPUT_DIR
Path to the kallisto index file generated from a reference file. If you have not indexed a reference file with kallisto, first create one with the "--ref" and "--index-out" arguments. (default: None)
Option is required.
Path to the reference file to create a kallisto index. (default: None)
Path to the output kallisto index. (default: None)
Path to the pair ended FASTQ files. (default: None)
Path to the directory to write output. (default: None)
Options specific to this tool
- --bias
- --fusion
- -b BOOTSTRAP_SAMPLES, --bootstrap-samples BOOTSTRAP_SAMPLES
- --num-threads NUM_THREADS
Perform sequence based bias correction. (default: None)
Search for fusions for Pizzly. (default: None)
Number of bootstrap samples. (default: 0)
Number of threads to use. (default: 4)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in the installation directory.
Do not override seccomp options for docker (default: None).
View compatible software versions.