Provided by: kissplice_2.4.0-p1-5ubuntu1_amd64
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.