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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Include more info from minced in the CRISPR annotations #29

Open tseemann opened 10 years ago

tseemann commented 10 years ago

Lizzy Wilbanks has left a new comment on your post "Prokka - rapid prokaryotic annotation":

Thanks for this great tool! So useful!! One thing that might be a nice addition for future releases would be providing more of the information from minced about the CRISPR regions - maybe as a separate output file? I've been re-running this to get the locations of the direct repeats and spacer sequences.

Posted by Lizzy Wilbanks to The Genome Factory at 31 July 2014 04:26

tseemann commented 9 years ago

You can extract the CRISPR coordinates from the GFF and GBK files as they are repeat_region feature types.

If you let me know what specific details you want maybe I can put them in the /product or /note field.

ewilbanks commented 9 years ago

Hi Torsten,

My comment was that, for my purposes, it would be useful to have prokka output the complete CRISPR info within the prokka gff file. The format that you get by running minced -gffFull gives coordinates of each repeat unit; this makes for a quick and easy display when I pop it up in a read alignmnent viewer (I'm using IGV) and want to look for variation in the spacer sequences between strains. Right now I just run minced seperately and add this in a separate track. No big deal, its just that this is info I usually want in addition to just knowing the coordinates of the CRISPR region.