Missing primers in multi amplicon sequencing

Question

[madalton]

Hello,

I've received some Illumina 2x250bp data with multiple overlapping amplicons (all in the same fastq files). The fastqc report looks great and so are the gels before. What I did next was to look for the primers with cutadapt to make sure the sequencing of each region was well balanced. I know which pcr primers have been used for each amplicon and so I used cutadapt.

Now, my issue is that except for the first amplicon, I could not find any primers (or close to none). I thought it might be either the sample or the run so I checked on several data from different samples and different runs and they all behave the same.

I've checked with the lab just to make sure they did not remove the primers before sending the data and they do not. Does anyone have ideas on what kind of scenario could lead to those primers missing in the fastqs ?

Thanks a lot

[madalton]

The amplicons should be around 450bp

[madalton]

I'm expecting to at least see one of the primers at the beginning of the read or am I missing something ?

What I mean is, I'm trying to look for a primer at the beginning of R1 and another one at the beginning of R2.