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hariszaf / pema

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
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Unexpected Singletons in Final Table despite removeSingletons set to "Yes" #58

Closed JustinePa closed 1 year ago

JustinePa commented 1 year ago

Issue When setting the "removeSingletons" parameter to "Yes" in PEMA, I'm noticing that many singletons still appear in the final output table (often hundreds of them towards the end of the table) while they should not be there.

Details I am using PEMA version 2.1.4, running it on ARMS data using the LifeWatch workflow on the Tesseract platform.

It would be appreciated if this behavior could be looked into, as it's crucial for the accuracy of our analyses to ensure that unwanted singletons are excluded when specified.

Thank you!

hariszaf commented 1 year ago

Hi @JustinePa !

Could you share your parameters file ?

JustinePa commented 1 year ago

Hi,

Sure, here it is: PemaParameters_v214_COI_2023 - Copy.txt

hariszaf commented 1 year ago

Hi, it seems we have forgot to update the parameters file in the analysis folder. I ll fix that asap.

If you are using the latest version of pema 2.1.4, then you should use this parameters file https://github.com/hariszaf/pema/blob/master/pema_docker_image/sanity_check/COI/parameters.tsv

Notice that there are now two parameters you need, the removeOligotons and another one for their number you d like to remove e.g doubleton

JustinePa commented 1 year ago

Thank you, I will try this!

hariszaf commented 1 year ago

Great! Give it a shot and please let me know if everything went fine 🚀