Perform preotein-RNA cross-linking experiments.
| pot. predecessor tools | RNPxl | pot. successor tools |
| RNPxlXICFilter | - |
The command line parameters of this tool are:
RNPxl -- Tool for RNP cross linking experiment analysis.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
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:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |