filtering field and pcr controls

User Support
1

Hello,
I have a few questions about filtering field controls as well as extraction/PCR controls from my data set. I have 10 different sample locations, each with replicates and a negative control. Is there a way to filter each location such that I am removing sequences from each site that are found in the field control?
For example:
CT_BLR_001
CT_BLR_002
CT_BLR_003
CT_BLR_004 (negative field control)--want to remove these sequences from other samples at this site.

I also have an extraction/PCR control for each day I completed these steps. For example:
CT_BLR_001
CT_BLR_002
CT_BLR_003
CT_BLR_004
CT_FLB_001
CT_FLB_002
CT_FLB_003
negative-1 (first day extraction/pcr control), want to remove these sequences from the samples I extracted/pcr on day 1.

I am unsure how this would work using the qiime filter options, and any help is appreciated!

4

Hi @amcrowell
Have you looked into decontam? I think this plugin is what you are looking for! Not the right link: https://github.com/jordenrabasco/q2-decontam .

See Jorden's Post below!

1 Like
5

Thanks for pointing people in the decontam direction @cherman2 !
However that repository is deprecated (I just made it private so not to mislead anyone) and all Decontam functionality has been folded into q2-quality-control

6

My Bad! Thanks for the correction!

1 Like