Galaxy

Get flanks

Select data:

Region:

Location of the flanking region/s:

Offset:

Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction.

Length of the flanking region(s):

Use non-negative value for length

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 +
```

../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 -
```

../static/operation_icons/flanks_ex2.gif