Including mock community in the Mothur MiSeq SOP pipeline
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17 months ago
spriyansh29 ▴ 30

I am running Mothur MiSeq SOP pipeline on Linux machine. Also, using mock-community (paired), which is in the same directory as my fastq files. While re-running the unique.seqs() after filtering, I am getting an error saying something is missing from the count table.

Command

unique.seqs(fasta=stability.trim.contigs.good.unique.good.filter.fasta, count=stability.trim.contigs.good.good.count_table)

Output/Error

Removing group: 31 because all sequences have been removed.

Removing group: 5 because all sequences have been removed.

Removing group: 57 because all sequences have been removed.

Removing group: 70 because all sequences have been removed.

Removing group: 71 because all sequences have been removed.

Removing group: 72 because all sequences have been removed.

I wonder if this is happening because the mock-community is in the same directory. Do we only use mock-community for error estimation steps as shown in Mothur MiSeq SOP pipeline and not in the previous steps?

Mothur Metagenomics Mock-community 16s • 338 views