Configure Inputs
Reference Assembly
GCF_030566675.1GTF Files
Genes and Gene Predictions
No gene models found.Paired-End Sequencing Data
Workflow
RNA-Seq Analysis: Paired-End Read Processing and Quantification
Description
Complete RNA-Seq analysis for paired-end data: Processes raw FASTQ data through adapter and bad quality removal (fastp), alignment with STAR using ENCODE parameters, gene quantification via multiple methods (STAR and featureCounts), and expression calculation (FPKM with Cufflinks/StringTie, normalized coverage with bedtools). Produces count tables, normalized expression values, and genomic coverage tracks. Supports stranded and unstranded libraries, generating both HTSeq-compatible counts and normalized measures for downstream analysis.
Species
Strain
MTb-Oman-3215873
Accession
GCF_030566675.1
Priority Pathogen
Tuberculosis