kissplice - detection of polymorphisms in RNA-seq data.
kissplice -h
kissplice [OPTION] [-r READFILES]
Detects alternative splicing events and other kinds of
polymorphisms from READFILES (in FASTA or FASTQ format).
- -h, --help
- Show this help message and exit.
- -r READFILES
- Input fasta/q read files (multiple, such as "-r file1 -r
file2...").
- -k KVAL
- k-mer size (default=25).
- -l LLMAX
- Maximal length of the shorter path (default: 2k-1).
- -m LL_MIN
- Minimum length of the shorter path (default 2k-8).
- -M UL_MAX
- Maximum length of the longest path (default 1000), skipped exons longer
than UL_MAX are not reported.
- -g GRAPH_PREFIX
- Path and prefix to pre-built de Bruijn graph (suffixed by .edges/.nodes)
if jointly used with -r, graph used to find bubbles and reads used
for quantification.
- -o OUT_DIR
- Path to store the results (default = ./results).
- -d PATH_TO_TMP
- Specific directory (absolute path) where to build temporary files (default
temporary directory otherwise).
- -t NBPROCS
- Number of cores (must be <= number of physical cores).
- -s
- Don't output SNPs (saves time).
- -v
- Verbose mode.
- -u
- Keep the nodes/edges file for unfinished bccs.
- -c MIN_COV
- Discard k-mers tha are present strictly less than this number of times in
the dataset. (default 2).
- -C MIN_RELATIVE_COV
- Discard edges with relative coverage below MIN_RELATIVE_COV expressed as a
percentage in [0,1). (default 0.02).
- -z GENOME_SIZE
- Estimated number of nodes in the De-Bruin Graph. (default =
1000000000).
- -e MIN_EDIT_DIST
- Classify as inexact repeats those bubbles whose paths' edit distance is
smaller than MIN_EDIT_DIST (default 3).
- -y MAX_CYCLES
- Maximal number of bubble enumerations in each bcc. If exceeded, no bubble
is output for the bcc (default 10000).
- --timeout
TIMEOUT
- Max amount of time (in seconds) spent for enumerating bubbles in each bcc.
If exceeded, no bubble is output for the bcc (default 900).
- --version
- Display program's version number and exit.