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rnaseq-qc

separate

Runs RNA-seq-specific post-alignment QC - strandedness inference, gene-body 5'-3' coverage, read distribution (exonic/intronic/intergenic), rRNA/globin/mitochondrial rate, transcript integrity (TIN), and saturation - with RSeQC, Qualimap, RNA-SeQC, and Picard. Use when validating RNA-seq libraries before quantification or differential expression, diagnosing degradation or gDNA contamination, or determining library strandedness. For raw-FASTQ QC use quality-reports; for UMI dedup use umi-processing.

When to use

• validating RNA-seq libraries before quantification
• diagnosing degradation or gDNA contamination
• determining library strandedness
• post-alignment QC on aligned BAM
• strandedness inference
• gene-body 5'-3' coverage
• read distribution (exonic/intronic/intergenic)
• transcript integrity (TIN)

When not to use

• raw-FASTQ QC
• UMI dedup
• quantification
• differential expression

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