SAMMate, a Graphical User Interface (GUI) RNA-seq analysis pipeline, allows biomedical researchers to quickly process Fasta/Fastq and 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.
Introduction
SAMMate is hosted by SourceForge.net. The project page is here. The source codes are available from the download page.
© Copyright 2009-2011 Computational Biology Group @UNO Computer Science. Created by Guorong Xu 2009.
Release Events:
- SAMMate 2.6.1 release - 5/28/2011
New features:
- 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.
Enhancements:
- 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.
Bug fixes:
- 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.
- SAMMate 2.6 release - 4/28/2011
New features:
- Supported Fastq or Fasta format by calling Bowtie to align short reads to a reference genome.
- Added time estimation of data processing.
- Added a dialog to configure Bowtie options.
- Added a dialog to configure signal map intervals.
- Added a dialog to configure the chromosome name mapping between gene annotation file and alignment data file.
Enhancements:
- In the transcript expression tab, added a column to display the transcript length.
- In the gene expression tab, changed the gene length to sum of exon length.
- In the Annotation Table tab, replaced transcript names with transcript Ensembl IDs.
- In the Annotation Table tab, added a column to display gene Ensembl IDs.
- Improved progress bar.
Bug fixes:
- When select gff3 gene annotation file, the transcript lengths are not calculated correctly.
features:
- Estimating genomic feature abundance at isoform level
- Calculating genomic feature abundance score at gene level
- Generating signal map for peak detection
- Generating wiggle files for visualization
- Generating alignment report
- Supported Fastq or Fasta format by calling Bowtie to align
short reads to a reference genome.
- Customize gene annotation file
- Customize chromosome name in output file
- SAM/BAM format conversion
- SAM/BAM file sorting
- Supports edgeR to detect differentially expressed genes and isoforms.
Publications:
(Please cite our papers if you use SAMMate to generate data
in your publications).
- 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
Contributors:
- Guorong Xu (Ph.D. Student), Dept. of Computer Science, UNO (The developer of SAMMate)
- Nan Deng (Ph.D. Student), Dept. of Computer Science, UNO
- Tin Nguyen (Ph.D. Student), Dept. of Computer Science, UNO
- Kristen Johnson (Master Student), Dept. of Computer Science, UNO
- Zhiyu Zhao (Computational Scientist), LONI Institute
- Dongxiao Zhu (Assistant Professor), Dept. of Computer Science, UNO (Principal Investigator)
