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?