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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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Option to handle read-through into primer for its sequences #69

Closed paulzierep closed 2 months ago

paulzierep commented 5 months ago

We want to use lotus2 to analyze ITS sequences. A common issue is the read-through into the opposite primer as described in the dada2 toturial: https://benjjneb.github.io/dada2/ITS_workflow.html Can lotus trim primers in such cases. I could not find it in the docs. Alternatively one could use cutadapt and then use lotus2 on the trimmed reads I guess... We will develop a toturial for such as case in Galaxy and I wanted to check what would be the best approach from your point of view ?

hildebra commented 5 months ago

Hey Paul, indeed, this case can happen and should be automatically processed in LotuS2. In the "ITS" sdm configs there should be the following flag set to "T":

this option should be "T" if your amplicons are possibly shorter than a single read in a paired end sequencing run (e.g. if the 16S amplicon length is 200bp in a 250x2 miSeq run, set this to "T"). This option increases runtime by 10%, if in doubt just set to "T". Requires LinkerPrimerSequence and ReversePrimer to be defined in mapping file.

AmpliconShortPE T

did this work as expected for you?

best, Falk

paulzierep commented 5 months ago

Ah perfect, that is probably what we need, will test if it trims as expected and let you know.