read_ngsfilter - Githubissues

metabaRfactory / metabaR

metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.

http://metabaRfactory.github.io/metabaR

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read_ngsfilter #34

Closed rongiergaetan closed 3 years ago

rongiergaetan commented 3 years ago

I noticed, I can't upload an NGSfilter file if one or more sample have the same forward and reverse tag, because the read_ngsfilter function doesn't take into account if they are a T instead of F in the 6th column.

lzinger commented 3 years ago

Hi. The setting you are describing should happen (i) if you have > 1 marker or primer pair or (ii) > 1 library in your ngsfilter file. metabaR has been designed to work with one single marker and library at a time because all errors (including sequencing ones) should be specific to the marker/primer pair and library. I would suggest you to split your ngsfilter file according either to the marker/primer pair, or library. Please let us know if it works with the recommendations above. thanks!

rongiergaetan commented 3 years ago

I have juste one marker pair on my ngsfilter, but different tags pairs. And if I just replace the T letter by F in the 6th column all is fonctionning. I think it's here in source code :

"additional <- gsub("F @ ", "", as.vector(input$additional))"

there aren't the command line to take into account the "T" instead of "F".

lzinger commented 3 years ago

Ok I see, sorry for the misunderstanding. Just corrected the bug, will push the function shortly. Thanks for noticing and reporting the problem!