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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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add remove_singletons option in OTU pipeline #47

Closed natgiot closed 1 year ago

natgiot commented 2 years ago

Currently, the option remove_singletons is only available in the ASV pipleline, please add it for the OTU one as well. Οr better, an option of filtering OTUs based on a user-defined filter :-) Thanks! Natassa

natgiot commented 2 years ago

Thanks Hari, hopefully the option of filtering based on a user-defined threshold will be available for both ASVs and OTUs in the next release! Natassa

hariszaf commented 2 years ago

Thanks @natgiot for the suggestion. I close the issue now and reg. ASVs we ll try to have it asap.

natgiot commented 1 year ago

Ηello there, We run a new pema with oligotron mode on for OTUs, but the final table file still contains OTUs with reads < our threshold (eg last OTU=2 reads, threshold was 7). Attached is the parameters file, the output is too big but grepping dinot show any major issue, the run completed OK. I can also send the finalTable.tsv, but I am not sure if I can attach here such big files (~10M) parameters0f.otu_align_151122_olig7.txt What do you think might have gone wrong? Thanks!

hariszaf commented 1 year ago

Hi @natgiot . Sorry for the late reply. Could you give it a shot using v.2.1.5 ? It's a beta version so you can find it as a Docker image only. If you are working on a Singularity environment, you may get this by running:

singularity pull --force --name pema.v.2.1.5_beta.sif docker://hariszaf/pema:v.2.1.5