SAMMate

SAMMate processes SAM and BAM files to compute short-read coverage, gene expression abundance, and base-wise whole-genome signal maps for next-generation sequencing (NGS) data analysis.

Key Features:

• Compatibility and Flexibility: Supports single-end and paired-end sequencing technologies and accepts standard and customized annotation files.
• Gene Expression Analysis: Calculates gene expression abundance scores using short reads from exons and exon-exon junctions across customized genomic intervals.
• Whole-Genome Signal Mapping: Generates whole-genome signal maps at base-wise resolution from alignment files.
• Data Visualization and Reporting: Exports wiggle files compatible with the UCSC Genome Browser and generates alignment statistics reports.
• Automation of Standard Procedures: Automates standard procedures in DNA-seq and RNA-seq data analysis.

Scientific Applications:

• microRNA (miRNA) target prediction: Uses short-read alignment information to support case studies predicting microRNA (miRNA) targets.
• Transcript quantification and genome-wide profiling: Enables quantification of transcript abundance and generation of genome-wide signal profiles for downstream biological interpretation.

Methodology:

Processes SAM/BAM files to calculate short-read coverage over genomic intervals, leverages standard and customized annotation files for gene expression scoring and whole-genome signal mapping, and exports wiggle files and alignment statistics for visualization and reporting.