returns flanking region/s for every gene get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} Whole feature Around Start Around End Upstream Downstream Both

This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. **Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue". ----- **Example 1** - For the following query:: chr22 1000 7000 NM_174568 0 + - running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**:: chr22 500 800 NM_174568 0 + .. image:: ../static/operation_icons/flanks_ex1.gif **Example 2** - For the following query:: chr22 1000 7000 NM_028946 0 - - running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**:: chr22 500 800 NM_028946 0 - .. image:: ../static/operation_icons/flanks_ex2.gif