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We developed a Graphical User Interface (GUI) software tool, SAMMate, for fast processing SAM files to automate some of more standard procedures in RNA-seq data analysis. Using standard or customized annotation files, SAMMate allows users to accurately calculate short read coverage for any genomic intervals. In particular, for RNA-seq data, SAMMate accurately calculates gene expression abundance scores for any customized genomic intervals by using short reads originating from both exons and exon-exon junctions. SAMMate also fast calculates a whole-genome signal map at the base-wise resolution, which is the required input for solving an array of bioinformatics problems. SAMMate exports a wiggle file for alignment visualization in UCSC genome browser, and an alignment statistics report. SAMMate is compatible with both single-end and paired-end sequencing technologies.
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