SAMSA

SAMSA annotates and analyzes metatranscriptomic RNA-seq data to quantify microbial transcriptional activity and functional profiles.

Key Features:

• MG-RAST integration: Leverages MG-RAST annotation servers to obtain functional and taxonomic annotations for metatranscriptomic reads.
• Transcriptional activity quantification: Quantifies organism-level transcriptional activity using mRNA counts and detects significant differences in organism activity and specific cellular functions between groups.
• Organism- and function-level breakdowns: Provides detailed breakdowns of transcription activity by organism and transcript function to identify abundant species and functional differences.
• Annotation summarization: Summarizes raw annotation results to facilitate evaluation of microbial community activities and interactions.

Scientific Applications:

• Stool metatranscriptome evaluation: Evaluates sequencing strategies and best practices for stool metatranscriptomes using pilot data and simulated subsets.
• Read length and pairing assessment: Assesses the impact of long reads (over 100 bp) and joined paired-end reads on annotation accuracy.
• Sequencing depth estimation: Estimates required sequencing depth, indicating approximately 40–50 million raw sequences per sample to achieve reliable annotated read counts.
• Differential activity detection: Identifies significant differences in organism transcriptional activity and specific cellular functions between control and experimental groups.

Methodology:

Uses MG-RAST for annotation; recommends ribosomal RNA depletion and removal of residual rRNA sequences; sequences in a 100 bp paired-end format with ~40–50 million reads per sample; quantifies mRNA counts to measure transcriptional activity and detect significant differences.