RNPxl

Perform preotein-RNA cross-linking experiments.

pot. predecessor tools	$\longrightarrow$ RNPxl $\longrightarrow$	pot. successor tools
RNPxlXICFilter	$\longrightarrow$ RNPxl $\longrightarrow$	-

Note: Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

RNPxl -- Tool for RNP cross linking experiment analysis.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  RNPxl <options>

Options (mandatory options marked with '*'):
  -in_mzML <file>*                             Input file (valid formats: 'mzML')
  -length                                      Oligonucleotide maximum length. (default: '4')
  -sequence                                    Sequence to restrict the generation of oligonucleotide chains.
                                               (disabled for empty sequence)
  -target_nucleotides                          Format:  target nucleotide=empirical formula of nucleoside 
                                               monophosphate
                                               e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS  where
                                               X represents e.g. tU
                                               or e.g. Y=C10H14N5O7PS where Y represents tG (default: '[A=C
                                               10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P]')
  -mapping                                     Format: source->target e.g. A->A, ..., U->U, U->X (default: 
                                               '[A->A C->C G->G U->U]')
  -restrictions                                Format: target nucleotide=min_count: e.g U=1 if at least one 
                                               U must be in the generated sequence. (default: '[A=0 C=0 U=0
                                               G=0]')
  -modifications                               Format: empirical formula e.g -H2O, ..., H2O+PO3 (default: 
                                               '[-H2O  -H2O-HPO3 -HPO3 -H2O+HPO3 +HPO3]')
  -peptide_mass_threshold <threshold>          Lower peptide mass (Da) threshold. (default: '600')
  -precursor_variant_mz_threshold <threshold>  Lower m/z (Th) threshold for precursor variant. (default: '260
                                               ')
  -CysteineAdduct                              Use this flag if the +152 adduct is expected.
  -in_OMSSA_ini <file>*                        Ini file for the OMSSA search engine
                                               (valid formats: 'ini')
  -in_fasta <file>*                            Fasta file for search result annotation
                                               (valid formats: 'fasta')
  -marker_ions_tolerance <tolerance>           Mz tolerance used to determine marker ions. (default: '0.05')
  -out_idXML <file>*                           IdXML output file
                                               (valid formats: 'idXML')
  -out_csv <file>*                             Csv output file
                                               (valid formats: 'csv')
                                               
Common UTIL options:
  -ini <file>                                  Use the given TOPP INI file
  -threads <n>                                 Sets the number of threads allowed to be used by the TOPP tool
                                               (default: '1')
  -write_ini <file>                            Writes the default configuration file
  --help                                       Shows options
  --helphelp                                   Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+RNPxlTool for RNP cross linking experiment analysis.

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'RNPxl'

in_mzML Input fileinput file*.mzML

length4 Oligonucleotide maximum length.

sequence Sequence to restrict the generation of oligonucleotide chains. (disabled for empty sequence)

target_nucleotides[A=C10H14N5O7P, C=C9H14N3O8P, G=C10H14N5O8P, U=C9H13N2O9P] format: target nucleotide=empirical formula of nucleoside monophosphate
e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU
or e.g. Y=C10H14N5O7PS where Y represents tG

mapping[A->A, C->C, G->G, U->U] format: source->target e.g. A->A, ..., U->U, U->X

restrictions[A=0, C=0, U=0, G=0] format: target nucleotide=min_count: e.g U=1 if at least one U must be in the generated sequence.

modifications[-H2O, , -H2O-HPO3, -HPO3, -H2O+HPO3, +HPO3] format: empirical formula e.g -H2O, ..., H2O+PO3

peptide_mass_threshold600 Lower peptide mass (Da) threshold.

precursor_variant_mz_threshold260 Lower m/z (Th) threshold for precursor variant.

CysteineAdductfalse Use this flag if the +152 adduct is expected.true,false

continuefalse Do not recreate intermediate files to continue after unexpected crash.true,false

in_OMSSA_ini Ini file for the OMSSA search engine
input file*.ini

in_fasta Fasta file for search result annotation
input file*.fasta

marker_ions_tolerance0.05 mz tolerance used to determine marker ions.

out_idXML idXML output file
output file*.idXML

out_csv csv output file
output file*.csv

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false