Removing primers before DADA2


I’ve sent this same problem through another account and Ben started helping me on how to solve it. But since I sen from the wrong account, I’m sending through my account so I can work on it.

This was my last post:

I’ve ran Qiime2 with DADA2 before and I usually would have around 30% of my sequences being filtered out after running DADA2, but this time I got only around 35% of my sequences back (meaning that 65% of my sequences are being filtered per sample).

This was the command I ran:

qiime dada2 denoise-paired --i-demultiplexed-seqs vanessa-demux-paired-end.qza --o-table vanessa_table_ee8 --o-representative-sequences vanessa-rep-seqs-ee8 --p-trim-left-f 10 --p-trim-left-r 10 --p-trunc-len-f 290 --p-trunc-len-r 235 --p-n-threads 30 --p-max-ee 8 --verbose

And this was my output:

                                                    input    filtered denoised  merged      non-chimeric

20-1_48_L001_R1_001.fastq.gz 413752 370970 370970 226078 153173
20-2_49_L001_R1_001.fastq.gz 631046 576952 576952 385678 237943
20-3_50_L001_R1_001.fastq.gz 709152 614104 614104 371633 209208
20-4_51_L001_R1_001.fastq.gz 683558 599355 599355 399690 285173
20-5_52_L001_R1_001.fastq.gz 711601 629273 629273 421946 258020
5-1_43_L001_R1_001.fastq.gz 659969 591283 591283 368305 186078

Ben asked this questions:

Can you clarify: What is the length of the amplicon you are sequencing? What are the primers? Are the primers on the reads?

And this is the answer:

We used the 341F-806R primer pair The merged amplicon is about 418 bp. From the same MiSeq run I had ran 2 other data sets that turned out fine. The data was generated with the adapter+primer PCR, so the primers may be in the read.

So, I would like to know how could I take the primers out of my sequences? Is there a tutorial or something similar that could help with this problem?

Thank you,


Correct me if I’m wrong, but is this the original thread (posting for cross-reference)?

Exactly Evan, this is the original one I posted in another account by mistake.

If you know the length of your primers you should be able to remove them during the denoising step using this command. See this post


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