CASH (Comprehensive alternative splicing hunting) is visualized and user-friendly software that aims to self-construct AS (alternative splicing) sites and detect differential AS events between samples of RNA-Seq data. CASH consists of two major stages: SpliceCons (Splice site Construction) and SpliceDiff (differential AS detection). By comprehensively reconstructing AS sites from RNA-seq data, SpliceCons increases the recognition of AS events considerably and subsequently, SpliceDiff uses two combined statistical methods to improve the detection of differential AS events.
  Different from our previous ASD program, we developed a new module named SpliceCons implemented into CASH and also refined the scripts to detect differential AS events. We recommend using CASH, which now replaces the original ASD version.

Input files

  CASH needs at least two types of files: bam files generated by TopHat or any other RNA-Seq mapping software, make sure the bam files were already be sorted and indexed; GFF3/GTF file corresponding to the gene annotations downloaded from NCBI, UCSC or Ensembl. Optionally, if the users want to retrieve the sequence around the splicing site, please load the genome sequence.


  This work was supported by China Postdoctoral Science Foundation [2013M541564], China Postdoctoral Science Special Foundation [2014T70439], Ministry of Science and Technology of China (973 Program 2012CB524900), and the National Natural Science Foundation (31170753 and 31070704).

Citing CASH

  1. Zhou X, Wu W, Li H, Cheng Y, Wei N, Zong J, Feng X, Xie Z, Chen D, and Manley JL et al. 2014. Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation. Nucleic Acids Res 42: 4019-4030.
  2. Wu W, Zong J, Wei N, Cheng J, Zhou X, Cheng Y, Chen D, Guo Q, Zhang B, Feng Y. CASH: a constructing comprehensive splice site method for detecting alternative splicing events. Briefings in Bioinformatics. Apr 2017. doi: 10.1093/bib/bbx034.
  3. Apoptotic Cell-Derived Extracellular Vesicles Promote Malignancy of Glioblastoma Via Intercellular Transfer of Splicing Factors