between assemblies and genomes liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch ucsc_tools

.. class:: warningmark Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary). .. class:: warningmark This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. BED comments and track and browser lines will be ignored, but if other non-interval lines are present the tool will return empty output datasets. ----- .. class:: infomark **What it does** This tool converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any. ----- **Example** Converting the following hg16 intervals to hg18 intervals:: chrX 85170 112199 AK002185 0 + chrX 110458 112199 AK097346 0 + chrX 112203 121212 AK074528 0 - will produce the following hg18 intervals:: chrX 132991 160020 AK002185 0 + chrX 158279 160020 AK097346 0 + chrX 160024 169033 AK074528 0 -