an interval file split_by_partitions.py ${GALAXY_DATA_INDEX_DIR} $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}

For detailed information about partitioning, click here_. .. _here: http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_All_Analysis_Groups Datasets are partitioned according to the protocol below: A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) 4. **Intronic Proximal** -- intronic and no more than 5kb away from an exon. 5. **Intergenic Proximal** -- between genes and no more than 5kb away from an exon. 6. **Intronic Distal** -- intronic and greater than 5kb away from an exon. 7. **Intergenic Distal** -- between genes and greater than 5kb away from an exon. ----- .. class:: infomark **Note:** Features overlapping more than one partition will take the identity of the lower-numbered partition.