bio-read-alignment-star-alignment

Paired-end alignment

STAR --runThreadN 8
--genomeDir star_index/
--readFilesIn reads_1.fq.gz reads_2.fq.gz
--readFilesCommand zcat
--outFileNamePrefix sample_
--outSAMtype BAM SortedByCoordinate

## Two-pass mode for better novel junction detection

STAR --runThreadN 8 \
    --genomeDir star_index/ \
    --readFilesIn r1.fq.gz r2.fq.gz \
    --readFilesCommand zcat \
    --outFileNamePrefix sample_ \
    --outSAMtype BAM SortedByCoordinate \
    --twopassMode Basic

Output gene counts (like featureCounts)

STAR --runThreadN 8
--genomeDir star_index/
--readFilesIn r1.fq.gz r2.fq.gz
--readFilesCommand zcat
--outFileNamePrefix sample_
--outSAMtype BAM SortedByCoordinate
--quantMode GeneCounts

Output: `sample_ReadsPerGene.out.tab` with columns:
1. Gene ID
2. Unstranded counts
3. Forward strand counts
4. Reverse strand counts