The RNA-seq pipeline delivers comprehensive transcriptome analysis from raw sequencing data (BAM or FASTQ) using user-supplied reference genomes and annotations. It is compatible with single-end or paired-end libraries. The pipeline includes quality assessment, expression quantification, and differential expression analysis.

Key Outputs:

  • Quality Control Metrics:

    • Percent rRNA contamination

    • Read mapping rates

    • Duplicate read counts

  • Expression Profiling:

    • Gene- and transcript-level quantification (TPM/FPKM)

    • Raw and normalized count matrices

  • Differential Expression:

    • Statistical results from DESeq2 or edgeR

    • Volcano plots and MA plots (optional)

    • Ready-to-interpret gene expression tables