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kissplice - Online in the Cloud

Run kissplice in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command kissplice that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


kissplice - detection of polymorphisms in RNA-seq data.

SYNOPSIS


kissplice -h
kissplice [OPTION] [-r READFILES]

DESCRIPTION


Detects alternative splicing events and other kinds of polymorphisms from READFILES (in
FASTA or FASTQ format).

OPTIONS


-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.

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