Finding adapters in sequences

Question

[genomics Newbie]

Hello,

How do you know whether you have found all the adapters in your 16S sequences for removal? I know how to identify and remove the universal primers for our 16S V3-V4 regions (341 forward and 805 reverse) but do not know how to identify any adapters for removal. Adapters may be different than the primers, right?

I reviewed the fastqc report for overexpressed sequences and found the primers, But how can I best find the adapters which require removal (in addition to the primers)?

Thank you!

[h.mon]

If you find and remove the primers, you will remove any left-over adapters. Which sequencing platform did you use? MiSeq with 2x250?, or 2x300bp?

[genomics Newbie]

Thank you for the speedy reply! Our sequences are 300 base pairs in length and we used paired-end reads sequenced with a MiSeq sequencer.. To confirm, if I remove the primers below I will automatically be removing the adapters? Can "primer" and "adapter" be used interchangably in documentation? I'm a "newbie" as you can see.

o Primer: 341F 5' -CCTACGGGNGGCWGCAG-3' o Primer: 805R 5' -GACTACHVGGGTATCTAATCC-3'

Answer 1

[GenoMax]

You can use bbduk.sh from BBMap Suite to scan/trim your data. BBMap includes a file adapters.fa in the resources folder of the software and contains all popular adapter sequences. There is a core sequence common to the adapters. Once that is detected in your reads the entire sequence to the right of the read is generally removed.

User guide for BBMap programs are available here.

Answer 2

[h.mon]

In general, you find adapters at the end of reads, when the insert length is shorter than the read. This is not your case for you particular primer pair, which will yield a ~500bp amplicon. So you just need to remove the PCR primers at the beginning of the reads. QIIME and Mothur both have commands for that.

[genomics Newbie]

It looks like your response may be a comment. Can you create a response so that i can accept this as the answer?