I am analyzing KIR gene sequencing data and have noticed the presence of certain genes, such as KIR2DS4, in samples that I know to be negative. I suspect that many non-specific reads are aligning to these genes, making it difficult to differentiate between specific and non-specific reads. I have extracted all reads that align to the KIR genes in my samples and would like to identify any patterns that may distinguish specific reads from non-specific ones.
I would appreciate any suggestions for methods or tools that could help me identify such patterns. I have considered using BLAST to identify similar sequences, but I am open to any other suggestions or insights on this issue. Thank you in advance for your help!