RNA-seq Quality Control

RNA-seq specific QC metrics beyond general read quality.

rRNA Contamination Detection

High rRNA content indicates failed rRNA depletion or polyA selection.

SortMeRNA

sortmerna \
    --ref rRNA_databases/smr_v4.3_default_db.fasta \
    --reads sample.fastq.gz \
    --aligned rRNA_reads \
    --other non_rRNA_reads \
    --fastx \
    --threads 8