SAMMate, a Graphical User Interface (GUI) RNA-seq analysis pipeline, allows biomedical researchers to quickly process SAM/BAM files and is compatible with both single-end and paired-end sequencing technologies. SAMMate automates some of more standard procedures in RNA-seq analysis.
Using either standard or customized annotation files, SAMMate allows users to accurately calculate the short read coverage of genomic intervals. In particular, for RNA-seq data SAMMate can accurately calculate the gene expression and isoform expression abundance scores for customized genomic intervals. SAMMate also exports raw read counts assigned to each gene and each isoform for detecting differentially expressed genes or isoforms using i.e. edgeR.
- Xu G, Deng N, Zhao, Z, Flemington EK, Zhu D. (2011) SAMMate: A GUI tool for processing short read alignment information in SAM/BAM format. Source Code for Biology and Medicine, 6:2.
- Deng N, Puetter, A, Zhang, K, Johnson, K., Zhao, Z, Taylor, C, Flemington, E and Zhu, D. (2011) Isoform-level microRNA-155 Target Prediction using RNA-seq. Nuc. Acid Res., doi: 10.1093/nar/gkr042