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SAJR-0.0 - Splicing Analyzer by Java and R

SAJR - home

SAJR is a simple java written read counter and R package designed to analyze splicing and gene expression based on RNA-seq data. SAJR is very fast, it takes about 1 min to parse 10 millions bam entries. It is easy to use and easy to understand: just download and calculate!

Additional functionalities, such as de novo annotation prediction and annotation converter are available.

SAJR consists of two blocks, that could be used independently:
  1. Java written read counter. It takes annotation and bam file as input and produces read counts for:
    • Genes. Or, more precisely, for constitutive (i.e. not alternatively spliced) part of genes
    • Junctions, i.e. number of reads that confirm given junction
    • Segments. Segment is a part of gene between two nearest splicing sites, it is smallest feature that can undergo independent splicing. Program counts two types of reads: inclusion reads (that confirms inclusion of the segments into transcript) and exclusion reads (that confirms exclusion of the segment from transcript): Inclusion and exclusion reads
    Output can be used in any other count-based applications (such as EdgeR or DE[X]Seq) or in the R-part of SAJR.
  2. R package that allows to visualize the data, test for differential splicing and differential expression (coming soon) by GLM with quasibinomial and quasipoisson distributions that allow to account for biological variability (overdispersion).
For more details please see manual page, or just download and run!
Developed by Mazin Pavel