Remove Primer in paired-end demultiplexed file

[SoilRotifer (Mike Robeson)]

Hi @mohsen_ej, if you search the forum, you'll come across many examples of how to use cutadapt. There are quite a variety of ways to leverage this tool.

You'll likely just want to specify your specific primer sequences not the entire construct. That is, your primers are likely these (anything after the ...GAGACAG):

--p-front-f CCTACGGGNGGCWGCAG \
--p-front-r GACTACHVGGGTATCTAATCC \

Here are a couple to get you started:

cutadapt - adapter vs front

Hello, I am working with 16S sequencing data generated using 515F-806R primers. 515F: GTGCCAGCMGCCGCGGTAA 806R: GGACTACHVGGGTWTCTAAT What is the difference between adapter and front in qiime cutadapt trim-paired? I got the following cut adapt parameters from a colleague that generated his 16S in the same DNA core that I did using the same primers. However, I am confused about the differences between adapter vs front and I am not sure if he used the correct sequence for each parameter. qiim…

q2-cutadapt output

Good news @jessica.song! I think I solved this. First, thank you for sending me the PDF describing the protocol. I noticed a key statement: pairs of primers (Fw-Rev or Rev-Fw) had to be present in the sequence fragments That is, this particular sequencing facility must expect mixed orientation reads. Therefore you need to enter in both primers for each of the --p-front-* commands (in 5’ - 3’ orientation). Like so: qiime cutadapt trim-paired \ --i-demu…

-Mike