What it does

Modifies the start and end coordinates of GFF data such that the new start and end position is based on a specified region size that is computed either from the existing start and end coordinates or centered on the midpoint between them.

Region expansion may result in the new start or end coordinates crossing the chromosome boundary. The chromosome start is set to 0 or 1 using the Start coordinate parameter. The end is retrieved from a file within the Galaxy environment that includes the length of chromosomes for all genome builds. If these files are missing, the end coordinate is set to 2147483647, which is the maximum value of a signed 32 bit integer. The Handle chromosome boundaries by parameter handles chromosome boundaries that are crossed by expanding the region using one of the following options.

• discarding the region - the region will be discarded and processing will continue with the next line in the dataset.
• keeping the region by limiting the expansion to not cross the start or end coordinate boundary - expansion will be restricted to not cross the chromosome's start or end coordinates for the current region.
• keeping the region by allowing the expansion to cross the start or end coordinate boundary - allow defined expansion, crossing the start boundary results in a negative start value.
• outputting an error - Stop processing and display an error.

Example

If the input dataset is:

chr1    genetrack       .       17      37      918     +       .       stddev=5.96715849116
chr1    genetrack       .       31      51      245     -       .       stddev=2.66582799529
chr1    genetrack       .       40      60      2060    +       .       stddev=2.7859667372

Setting start coordinate to 1 and resizing the coordinate window by 13 from the computed midpoint of the start and end coordinates produces:

chr1    genetrack       .       14      40      918     +       .       stddev=5.96715849116
chr1    genetrack       .       28      54      245     -       .       stddev=2.66582799529`
chr1    genetrack       .       37      63      2060    +       .       stddev=2.7859667372