GobyWeb Frequently Asked Questions (FAQ)

How can I add a new reference database?

Please email us and let us know which genome reference you would like to add. We have automated scripts to import genomes and annotations available through Ensembl.org. Please indicate the species and the reference assembly number your project require.

Goby strips read identifiers from my inputs. How can I get around that?

By default, read identifiers are stripped off the input because identifiers take up space and are not used by the Gogy alignment pipeline. Goby relies on read indices rather than identifiers to distinguish between different reads in the input. This is more time and space efficient. If you ever needed to preserve read identifiers you could do this with the -x option. Alternatively, you could keep a mapping between read identifier and read index by removing the sequence from the input (keeping only read identifier and read index in the compact file). This can be done with:

• java -jar goby.jar -m reformat-compact-reads -x --exclude-sequences <file.compact-reads>

Are alignments produced by GobyWeb sorted and indexed?

Yes. Full genome alignments are sorted and indexed by genomic location. Downloads include the basename.index file which contains the Goby alignment index. Transcript alignments are neither sorted nor indexed.