I work on NGS data (illumina paired ends reads) coming from a full extract of RNA (metagenomic). We are interested in the viral fraction of this extract.
I observed a contamination with a PCR amplicon. This contamination has been identified as coming from a PCR result that we used to make near the library preparation. So I know exactly the primers used in the PCR.
The problem I have is that these PCR products are exactly the type of sequence I want from my extract (identifying part of the virus). So I have some "false positive" and some misidentification of viruses present in the extract.
I have thought about removing all reads containing primer sequences but it leads to a gap in my data and I can't identify the viruses in my extract anymore. I am thinking that all of the read pairs that begin before or end after my primers are "true-positives" and I would really like to keep them (even having the primer sequence in them).
Do you know any tool that can help me in that situation? i.e. removing reads containing a sequence but only if it begins with it.
If the tool can also handle the degeneration of my primer it would be perfect.
An example of primer I used is
Complementary information (asked in comments)
I have around 30 million read pairs (60 millions reads in total). Contamination reads are between 200.000 to a 1 millions reads (depending on sample). "true" reads (not from the contamination) represent around 0.5% of the contamination.