OTU table

[Fatemeh-qasemnejad]

Hi,
I am trying to generate an OTU table using SingleM, but I think I am using the wrong command.

I ran:

singlem pipe
--reads sample_R1.fastq.gz sample_R2.fastq.gz
--otu-table output_directory/sample_OTUtable.csv
--threads 16

I expected an OTU table, but instead I got output like this:

gene sample sequence num_hits coverage taxonomy

This looks like gene-level sequence hits, not an OTU table.
Also, the genes are not unique, which makes me think something is wrong.

My question:
How should I correctly run SingleM to generate an OTU table?

Thank you!

[wwood]

Hi, I think so too. Using -reads like that will treat them both as forward, as if from different samples. Use -1 and -2 for instance. Also, I think you want the -p option. See https://wwood.github.io/singlem/Glossary Hth -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

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________________________________ From: Fatemeh-qasemnejad ***@***.***> Sent: Friday, November 28, 2025 7:42:32 PM To: wwood/singlem ***@***.***> Cc: Subscribed ***@***.***> Subject: [wwood/singlem] OTU table (Issue #268) [https://avatars.githubusercontent.com/u/246649974?s=20&v=4]Fatemeh-qasemnejad created an issue (wwood/singlem#268)<#268> Hi, I am trying to generate an OTU table using SingleM, but I think I am using the wrong command. I ran: singlem pipe --reads sample_R1.fastq.gz sample_R2.fastq.gz --otu-table output_directory/sample_OTUtable.csv --threads 16 I expected an OTU table, but instead I got output like this: gene sample sequence num_hits coverage taxonomy This looks like gene-level sequence hits, not an OTU table. Also, the genes are not unique, which makes me think something is wrong. My question: How should I correctly run SingleM to generate an OTU table? Thank you! ― Reply to this email directly, view it on GitHub<#268>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5H4Q45L4BQJFQG5GDD37AKIRAVCNFSM6AAAAACNORSII6VHI2DSMVQWIX3LMV43ASLTON2WKOZTGY3TIMRVHAZDEMI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>