Aptamers have evolved as a viable alternative to antibodies in some research areas in recent years. High throughput sequencing (HTS) has revolutionized the aptamer research by increasing the number from few reads using Sanger sequencing to millions of reads per sample at the fraction of cost. Despite the availability and advantages compared to Sanger sequencing - there are only 50 aptamer sequencing samples available as of now on public databases and most of them comes from only 2 studies. HTS data for aptamer research are mostly used to compare sequence enrichment between subsequent selection cycles. This approach does not take full advantage of HTS because enrichment of sequences during selection can be due to inefficient negative selection. Here we present differential binding cell-SELEX workflow that adapts bioinformatics tools mainly used for functional genomics to achieve more informative metrics about the selection process. Method can be used to characterise not only enrichment of sequences between cycles, but also differential binding of enriched sequences to target and control cells used for SELEX experiment. We demonstrate our approach by performing aptamer selection against clear cell renal cell carcinoma (ccRCC) cell line using cell line from healthy kidney tissue for negative selection.