Is there any way to remove entire reads from a FastQ file IFF the first "x" bases are of bad quality? I will FastQC the whole read later for a cumulative score but right now I am interested in the barcode region.
Basically I fear barcode contamination and I do not wish to keep the reads which might have lower quality scores in the barcode region / first 8-10 bp. I do not want to trim the reads but completely remove them.
I tried fastx barcode splitter but it searches for the barcode sequence while I want to search the quality of the barcode sequence.
Really sorry if my words sounded redundant but I really hope there is some tool which can do this so I can integrate it in a pipeline.