Question: Using BBDuk to trim degenerate primers off of amplicon reads
1
gravatar for t89oconnell
2.4 years ago by
t89oconnell10
t89oconnell10 wrote:

I'm using BBDuk to trim adapters as well as primers with a bunch of degenerate bases off of amplicon reads and I want to confirm that BBDuk works with all the different IUPAC degenerate base codes ("R", "Y", "S", "W", "K", "M", "B", "D", "H", "V") and not just "N". The BBDuk documentation only shows an example using "N", so I wanted to check on this so I'm sure I get all the primers trimmed off properly. I am using settings of k=21, mink=12, hdist=1, and I'm using the included adapters reference file as well as a custom fastq reference file containing my set of tagged forward and reverse primers and the untagged primers. Any input from the community is much appreciated. Thanks.

bbduk • 1.3k views
ADD COMMENTlink modified 2.4 years ago by genomax91k • written 2.4 years ago by t89oconnell10
1
gravatar for genomax
2.4 years ago by
genomax91k
United States
genomax91k wrote:

From BBDuk guide page.

Matching degenerate sequences such as primers:

bbduk.sh in=reads.fq out=matching.fq literal=ACGTTNNNNNGTC copyundefined k=13 mm=f

This will clone the reference sequences to represent every possibility for the degenerate bases (Ns and other non-ACGT IUPAC symbols). For example, this would create ACGTTAAAAAGTC, ACGTTAAAACGTC, ACGTTAAAAGGTC, and so forth (all 1024 possibilities). If you are interested in seaching for new life by mining shotgun metagenomic reads for 16s sequences that do not quite match your primers… this (and hdist) might be a good place to start! But it’s also useful for adapters with barcodes.

ADD COMMENTlink written 2.4 years ago by genomax91k
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