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hildebra / lotus2

Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
http://lotus2.earlham.ac.uk/
GNU General Public License v3.0
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blast output #60

Closed johnrandallia closed 5 months ago

johnrandallia commented 5 months ago

I would like to use the blast output in MEGAN, but the conversion from blast to rma fails. The blast output should be tab separated and with 12 columns. I get 11 columns (without bitscore) from Lotus2?

johnrandallia commented 5 months ago

The 11. Column seems kind of odd as well? If I use a dummy value for the 12. column it still doesn't assign any taxonomy to the results. Only if I replace the 11. column with e.g. "0.0" it seems to get it right.

hildebra commented 5 months ago

Hey John, lotus2 uses custom output columns, it's not a m8 format. These are defined as: 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send qlen' You can always check the extact mapping parameters used by looking in "LotuSLogS/LotuS_cmds.log" for the mapping command, e.g. lambda3 by default. you can also rerun the lambda command with your required output format as arguments to lambda, but since a lot of temp files will be deleted after lotus2 is finished this will probably not work after a lotus2 run. Instead, you would want to abort lotus2 while it is executing the alignment, and then replace the lambda command with your own version of it (and run it). hth, Falk