Drag out certain reads based on SingleM classification?

[NebulaSL]

Hi SingleM team! I was wondering is it possible to drag out certian reads or know which reads are based on the taxonomy classification of SingleM? I am current consider using a smaller group of reads for metagenomic assembly/binnning process and curious about whether it is possible to use singleM to perform the first step.

Thanks in advance!

[wwood]

Hi,

If you run pipe with --otu-table and --output-extras it gives you the reads contained within each OTU. Is that what you mean?

[NebulaSL]

Hi Ben, Thanks for the quick response. In the OTU table that you mentioned only contains 60 bases since singlem classified taxonmy according to this right? I mean like if there is a way I can know the original reads (150 bp reads by Illumina sequencing)? Thanks a lot! Best, Shiyi

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On Jul 9, 2024, at 19:44, Ben J Woodcroft ***@***.***> wrote: Hi, If you run pipe with --otu-table and --output-extras it gives you the reads contained within each OTU. Is that what you mean? — Reply to this email directly, view it on GitHub <#189 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BB22NE67E6KDTJHZ6MR2BYLZLQOO3AVCNFSM6AAAAABKS4DZMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJYGMYDMOBWGQ>. You are receiving this because you authored the thread.

[wwood]

With output extras there is another column with the full read. It is also in the archive otu table output if you prefer json.

[NebulaSL]

Thanks a lot! I will give it a try!

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On Jul 9, 2024, at 20:07, Ben J Woodcroft ***@***.***> wrote: With output extras there is another column with the full read. It is also in the archive otu table output if you prefer json. — Reply to this email directly, view it on GitHub <#189 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BB22NEYADJIANXFATZODFVLZLQRGZAVCNFSM6AAAAABKS4DZMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJYGM2DEOBZHA>. You are receiving this because you authored the thread.