I recently got several exomes but the FastQC suggested that there might be adaptor sequencing contamination showed on Kmer content. I used clip adaptor and filter the read by quality but then I when I try to use BWA to align, it failed.
If I use non-clip fastq, BWA works. Any suggestion how to fix this problem?
Or perhaps, it doesn't matter as the contaminated reads will not be aligned properly anyway?
Thanks for your opinion or suggestion in advance.