Repeat masked vs Repeat unmasked genome assembly

Question

[lukhanyomakhabane]

Hi everyone Can you please assist me here, which assembly is advisable (between repeat masked and repeat unmasked assembly) to use when you want to perform BLAST searches against genome assembly ( searching for genes in a particular genome). MyCocosm provides repeat masked and repeat unmasked assembly, so I'm not sure which one to use, your help would be greatly appreciated.

Answer 1

[lieven.sterck]

I would start with the masked version (given that it has been masked OK, that is accurate, not too much false positives, ...) , that will 'free up ' space in your blast hit list for the real meaningful hits (== the protein-coding ones for instance) . If you use the unmasked version a lot of hits against TEs will be reported.

If you notice when using the masked version that you miss obvious hits, you can switch to the unmasked one.

[lukhanyomakhabane]

Alright, thank you so much for this information.

[mks002]

To add on, you can also try searching for pseudogenes (from the annotation file i.e the gff file) and mask the pseudogenes to get more specific hits.