GFF3 of blast hits

Want to see where in a genome spacers hit? Make a GFF3 file of the spacer blast hits to that genome, then view it in a genome view (jbrowse for example).

GFF3 of all spacers that hit E.coli

$ CLdb_spacerBlast2GFF.pl -d CLdb.sqlite -staxon_name "E.coli" > ecoli_hits.gff

GFF3 of all spacers that hit FIG|2209.27

$ CLdb_spacerBlast2GFF.pl -d CLdb.sqlite -staxon_id 2209.27 > 2209.27_hits.gff

Adding the gff3 as a track in jbrowse

jbrowse setup

See: jbrowse website

adding gff file to ECOLI genome in jbrowse

This is assuming that the genome has been added to the directory: "/var/www/jbrowse/data/ECOLI/"

$ CLdb_spacerBlast2GFF.pl -d CLdb.sqlite -staxon_name "E.coli" > ecoli_hits.gff

$ flatfile-to-json.pl -gff ecoli_hits.gff --tracklabel spacer_blast --out /var/www/jbrowse/data/ECOLI/