create a random set of intervals random_intervals_no_bits.py $regions $input2 $input1 $out_file1 ${input2.metadata.chromCol} ${input2.metadata.startCol} ${input2.metadata.endCol} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} $use_mask $strand_overlaps ${GALAXY_DATA_INDEX_DIR} No Yes Any Across Strands None .. class:: warningmark This tool currently only works with ENCODE data from genome builds hg16 or hg17. ----- .. class:: infomark **Note:** If you do not wish to mask a set of intervals, change the Use Mask option to No, this option will override any Mask files selected. ----- **Syntax** This tool will attempt to create a random set of intervals that mimic those found within your source file. You may also specify a set of intervals to mask. **Allow overlaps** options * **Across Strands** - random regions are allowed to overlap only if they are on different strands. * **Any** - all overlaps are allowed. * **None** - no overlapping regions are allowed. **Regions to use** options * Bounding region of interest based on the dataset build. ------ **Citation** If you use this tool, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_