What it does

For every interval in the interval dataset, this tool fetches the closest non-overlapping upstream and / or downstream features from the features dataset.

Note:

Every line should contain at least 3 columns: chromosome number, start and stop coordinates. If any of these columns is missing or if start and stop coordinates are not numerical, the lines will be treated as invalid and skipped. The number of skipped lines is documented in the resulting history item as a "data issue".

If the strand column is missing from your input interval dataset, the intervals will be considered to be on positive strand. You can add a strand column to your input dataset by using the Text Manipulation->Add column tool.

For GFF files, features are added as a GTF-style attribute at the end of the line.

Example

If the intervals are:

chr1 10   100  Query1.1
chr1 500  1000 Query1.2
chr1 1100 1250 Query1.3

and the features are:

chr1 120  180  Query2.1
chr1 140  200  Query2.2
chr1 580  1050 Query2.3
chr1 2000 2204 Query2.4
chr1 2500 3000 Query2.5

Running this tool for Both Upstream and Downstream will return:

chr1 10   100  Query1.1 chr1 120  180  Query2.1
chr1 500  1000 Query1.2 chr1 140  200  Query2.2
chr1 500  1000 Query1.2 chr1 2000 2204 Query2.4
chr1 1100 1250 Query1.3 chr1 580  1050 Query2.3
chr1 1100 1250 Query1.3 chr1 2000 2204 Query2.4