salmon-rna-quantification

What problem does it solve?

This Skill automates the process of quantifying gene and transcript expression levels from RNA-sequencing data, enabling downstream differential expression analysis.

Core Features & Use Cases

• Ultra-fast Quantification: Utilizes quasi-mapping for rapid transcript abundance estimation, significantly faster than alignment-based methods.
• Bias Correction: Automatically corrects for sequence-specific and GC-content biases for more accurate quantification.
• Downstream Integration: Outputs compatible with tools like tximeta and pydeseq2 for differential expression analysis.
• Use Case: Analyze RNA-seq data from a drug treatment experiment to identify genes that are significantly up- or down-regulated.

Quick Start

Use the salmon-rna-quantification skill to build an index from the transcriptome FASTA file and then quantify paired-end reads from sample_R1.fastq.gz and sample_R2.fastq.gz.