crux create-index

Usage:
crux create-index [options] <protein input file> <index name>
Description:
Given a protein fasta sequence database as input, generate an index of all of its peptides and save it to disk. Optionally, the index may also include decoy peptides to be used for post-processing commands such as crux percolator, crux q-ranker crux compute-q-values or crux barista. The index can be provided as input to crux search-for-matches instead of the fasta file to speed up the search.

Input:

Output: Options: Parameter file options: Increasing the file limit: Known Bugs

In cygwin, the --overwrite T option does not work. A temporary directory is created with the new index but fails to be re-named correctly. As a work-around, delete the existing index and rename the new temporary index with the correct name.


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