mothur

Assessing error rates using mock communities

#1

Dear Mothur Help Team,

I would be most grateful for your help with regards to assessing error rates using mock community. I have been using the MiSeq SOP tutorial (which is so amazingly detailed and clear by the way!) on my own small dataset, but am stuck on how to specify my Positive control/mock community in the get.groups command.

I have the fastq files of my samples:
|NCext|E12-0_S93_L001_R1_001.fastq|E12-0_S93_L001_R2_001.fastq|
|PCext|F12-0_S94_L001_R1_001.fastq|F12-0_S94_L001_R2_001.fastq|
|NSEQ009|G12-0_S95_L001_R1_001.fastq|G12-0_S95_L001_R2_001.fastq|
|NSEQ013|H12-0_S96_L001_R1_001.fastq|/data/combined4runs/H12-0_S96_L001_R2_001.fastq|

PCext is the positive control with the mock communities. How do I specify this?

Thank you very much for your help!

#2

If your mock community is called PCext in the files file, then when you run get.group you would use group=PCext instead of group=Mock. The outputted files are suitable for input to seq.error. Also, remember to do the same thing when you do remove.groups.