Filtering out Illumina primer sequence

[kevpar]

Hi,

Like many I am new to NGS. Currently I'm running through the analysis pipeline for my RNAseq data and find through a quality check in FastQC that I have a number of overepresented sequences, all of which are Illumina primers.

I have FASTX for preprocessing of this data but there doesn't seem to be an obvious way of filtering these reads out. I was thinking of using the clipper tool but I don't understand how I can get more than one of these sequences filtered at a time.

This is what I was thinking of using in FASTX but I can't envision how to get rid of more than one primer at a time

fastx_clipper [-a overepresented sequence] [-D] [-n] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE]


Is there a tool for this type of filtering I'm missing? Do most of you even perform this type of filtering? Is it acceptable to just move on to mapping without this type of filtering?

[pbluescript]

This is the tool I use and you need to do this if you want to map as many of your reads as possible.
However, I'm confused about your question. You can filter them out one at a time with a simple shell script that runs the fastx_clipper with the separate primer sequences sequentially.