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
kissplice - detection of polymorphisms in RNA-seq data.
kissplice [OPTION] [-r READFILES]
Detects alternative splicing events and other kinds of polymorphisms from READFILES (in
FASTA or FASTQ format).
Show this help message and exit.
Input fasta/q read files (multiple, such as "-r file1 -r file2...").
k-mer size (default=25).
Maximal length of the shorter path (default: 2k-1).
Minimum length of the shorter path (default 2k-8).
Maximum length of the longest path (default 1000), skipped exons longer than UL_MAX
are not reported.
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.
Path to store the results (default = ./results).
Specific directory (absolute path) where to build temporary files (default
temporary directory otherwise).
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.
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).
Estimated number of nodes in the De-Bruin Graph. (default = 1000000000).
Classify as inexact repeats those bubbles whose paths' edit distance is smaller
than MIN_EDIT_DIST (default 3).
Maximal number of bubble enumerations in each bcc. If exceeded, no bubble is output
for the bcc (default 10000).
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.
Use kissplice online using onworks.net services