add remove_singletons option in OTU pipeline about pema HOT 4 CLOSED

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

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

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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!

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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

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