Drop fastq.gz files here.

They must contain _R1* and _R2* and will be processed as pairs if multiple are uploaded.
     Select an genome: 

       

     

RNA Sequencing Pipeline Overview

  • Handles paired-end Illumina RNA sequencing data
  • Supports both bacterial and eukaryotic genomes
  • Automatic detection of organism type for parameter optimization

  • Uses Bowtie2 for bacterial genomes with optimized parameters
  • Supports local alignment with dovetail detection
  • Generates sorted and indexed BAM files
  • Handles unaligned reads separately for quality control

  • Uses featureCounts for gene expression quantification
  • Separate counting of rRNA reads
  • Supports strand-specific protocols
  • Minimum overlap length of 30bp for read assignment

  • MultiQC report generation for quality metrics
  • Alignment statistics and mapping quality assessment
  • Results delivered via email upon completion
  • Automated cleanup of intermediate files