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Repeat masked vs Repeat unmasked genome assembly

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.

blast
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updated by mks002 mks002 • written by lukhanyomakhabane • lukhanyomakhabane

1 answer

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.

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written by lieven.sterck lieven.sterck

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.

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written by mks002 mks002

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