From Raw Reads to Gene Counts
| Step | Command |
|---|---|
| Quality Control | fastqc *.fq |
| Trimming | cutadapt -q 20 -m 30 -o trimmed.fq input.fq |
| Alignment | hisat2 -x index -U trimmed.fq -S aligned.sam |
| SAM → BAM | `samtools view -bS aligned.sam |
| BAM Index | samtools index aligned.bam |
| Quantification | featureCounts -a annotation.gtf -o counts.txt aligned.bam |