bio-workflows-rnaseq-to-de

Batch processing

for sample in sample1 sample2 sample3; do fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz
-o trimmed/${sample}_R1.fq.gz -O trimmed/${sample}_R2.fq.gz
--detect_adapter_for_pe
--html qc/${sample}_fastp.html done

**QC Checkpoint 1:** Check fastp reports
- Q30 bases >80%
- Adapter content <5%
- Duplication rate reasonable for library type

## Build index (once per transcriptome)

salmon index -t transcriptome.fa -i salmon_index -k 31

## Quantify each sample

for sample in sample1 sample2 sample3; do
    salmon quant -i salmon_index \
        -l A \
        -1 trimmed/${sample}_R1.fq.gz \
        -2 trimmed/${sample}_R2.fq.gz \
        -o quants/${sample} \
        --validateMappings \
        --gcBias \
        --seqBias \
        -p 8
done

QC Checkpoint 2: Check Salmon logs

• Mapping rate >70%

• 10 million reads mapped