Adding Searchable Features

This page describes how to allow JBrowse to find and display user loaded features using its native search functionality.

Building Searchable Names From GFF Files

1. Navigate to /home/bencap/jbrowse_track_building and add any new data to the appropriate raw/ directory.
2. Run the name generation script with a command similar to the one below:

python3 bin/build_gff_names.py --in /web/docs/bbqs_master/raw/PROKKA_06192020.gff --strain BBQS859

3. Verify the file names.txt was generated in your ./data/tracks/BBQS859/Prokka/NZ_QPEQ01000001.1/ directory.
4. Copy the new name file to the appropriate data directory with a command like

cp -r ./data/tracks/BBQS859/Prokka /web/docs/bbqs_master/data/tracks/

5. Index the name file with the command

./bin/generate-names.pl --out /web/docs/bbqs_master/data/

6. Reload the browser.

Building Searchable Names from BED Files

1. Navigate to /home/bencap/jbrowse_track_building and add any new data to the appropriate raw/ directory.
2. Run the name generation script with a command similar to the one below. For the label field, you should use the label value present in trackList.json for the track you are generating names for.

python3 bin/build_bed_names.py --in /web/docs/bbqs_master/raw/bbqs859_chr1.effectors_for_browser.bed --strain BBQS859 --label 'effectiveELD etc'

3. Run the above command for the other chromosome.
4. Copy the new name file to the appropriate data directory with a command like

cp -r ./data/tracks/BBQS859/<label> /web/docs/bbqs_master/data/tracks/

5. Index the generated name files with the command

./bin/generate-names.pl --out /web/docs/bbqs_master/data/

6. Reload the browser.