Convert BED to GFF
File input (BED)
This script processes BED-type files so make sure your input is properly formatted and uses the appropriate .bed extension if you are working from the GUI.
Output (GFF)
The converted file is named the same as its corresponding input filename by default (just swap extension for .gff) in GFF-style format with the id (4th) column in the BED file used for details stored as the details column (9th) in the new BED file. Score columns map accordingly.
Output GZip
Toggling this allows the user to write output to a compressed file format using a general compression (gzip) which has the added advantage of speeding up the execution time by shrinking the I/O load (esp for large output). The .gz extension will be appended as appropriate.
Command Line Interface
Usage:
java -jar ScriptManager.jar coordinate-manipulation bed-to-gff [-hsV] [-o=<output>]
<bedFile>
Positional Input
This tool takes a single BED file for input.
Output Options
| Option | Description |
|---|---|
| -o, --output | specify output filename (default name will be same as original with .gff ext) |
| -s, --stdout | output gff to STDOUT |
-z, --gzip | gzip output (default=false) |