rnaseq-pipeline

Step1: Alignment

STAR --genomeDir [path-to-genome-index] --readFilesIn Sample_R1.fastq.gz Sample_R2.fastq.gz --readFilesCommand zcat --runThreadN 4

This will output bam files.

Step2: quantification

featureCounts -a genes.saf -o output.counts [BAM FILES] -F SAF -T 8

quality checks

fastqc *.fastq.gz # check fastq files samtools flagstat [BAM FILES] # check