First make your project directory, and make a fastq directory in the project folder. project/fastq. Put all of your fastq files in the project/fastq folder. Fastq files could be in .fastq or .gz or .bz2 format. Name your fastq files either as *.fastq.[gz/bz2] (single read) or *_R1.fastq and *_R2.fastq (paired-end reads).

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

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

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