Alternative splicing is a special biological process.It leads to protein diversity by allowing a single gene generate multiple mRNA products.Current studies have demonstrated that alternative splicing play a crucial role in the eukaryote.Aberrant splicing will result in developmental abnormalities,hereditary diseases,or cancer.The prediction of splice sites and alternative splicing sites is very important for the research of gene expression regulation in eukaryotes.With the development of next generation sequencing technology,RNA-seq data has been used to identify specific splice sites in different tissue or cell lines.TopHat is a fast splice junction mapper for RNA-Seq reads[1].It can align RNA-Seq reads to genomes using Bowtie and identify splice junctions between exons by analyzing the mapping results.Based on the RNA-Seq data of K562 and GM12878,we built cell-line-specific splice sites database to study alternative splicing of genes in human.Three samples (SRR521468,SRR534174,SRR534175) of GSM958731 for K562 were downloaded from the Genome Expression Omnibus(GEO)[2].