Output files

Output Files

CRUSH outputs 4 files, each of which starts with the prefix that you specified with the -o option. The file name endings are:

CRUSHparameters.txt: Contains a simple record of the parameters and files that you used. In the following names, the outputprefix and resolution are replaced with whatever you specified with the -o and -r options.

outputprefix_mergedCrush_resolution.bedgraph: This is the main output file containing the scores for A (positive) and B (negative). Note that unlike eigenvector, you do not need to flip these calls because A is always positive and B is always negative.

outputprefix_mergedqvalue_resolution.bedgraph: This bedgraph track contains an estimated q-value for each bin's score.

outputprefix_mergedCrush_resolution_qfiltered.bedgraph: This bedgraph track contains the CRUSH calls for only bins that pass the q-value filter. The q-values tend to be overly stringent though.