SAMMate is a free and easy to use GUI software tool for processing SAM files. SAMMate allows users to accurately estimate gene expression scores using short reads to generate wiggle files for visualization in UCSC genome browser and an alignment statistics report.
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.
Here are some key features of "SAMMate":
· Calculating genomic feature abundance score using RNA-seq data
· Generating signal map for peak detection
· Generating wiggle files for visualization
· Generating alignment report
· Customize gene annotation file
· Customize chromosome name in output file
· Java 1.6 or later
What's New in This Release: [ read full changelog ]
· Supports edgeR to detect differentially expressed genes and isoforms.
· Supported simultaneous multiple instances of SAMMate runs.
· Users can export P-values to transcript expression file.
· In the Work Space, added two group tabs to separate files into two groups.
· In the Options dialogue, added R Options to configure R information.
· When input SAM and BAM files simultaneously, missing information in Report.html
· Fixed the 32bit problem on Linux 64bit OS.
· Fixed the parsing problem of some GFF3 annotation files.