Extract Hits

Extracting hit sequences and their flanks using the DIGS tool

Working within the framework of the DIGS tool (i.e. using SQL to query DIGS results, and reclassifying sequences through merging and updates reference libraries) can provide many useful insights into the distribution and diversity of a given genome feature.

For further investigations, however, it will often be necessary to export sequences from the DIGS screening database so that they can be analyzed using other kinds of bioinformatic and comparative approaches.

As well as extracting the sequence matches themselves, it is often helpful to extract the upstream and downstream flanking sequences.

To do this, run the digs_tool.pl script using the -d=6 option, and providing a tabular file containing locus data using the -i option as illustrated here:

giff01r@Alpha:~/DIGS/DIGS-tool$ ./digs_tool.pl -d=6 -i loci.tsv