Provided by: kissplice_2.4.0-p1-4_amd64 bug


       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).

              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).

              Display program's version number and exit.