joowkim · August 3, 2018 06:19
diff --git a/star-genes-count.txt b/star-genes-count.txt
 STAR_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/"
 INPUT_DIR="00_raw_fastq"
 OUTPUT_DIR="01_alignment_genes_count"
 GTF="/home/mRNAseq/ref/gencode/human/GRCh37.19/gtf/gencode.v19.annotation.gtf"
 RSEM_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/GRCh37.p13.genome"

 mkdir -p $OUTPUT_DIR

 cat samples.list | parallel --jobs 1 "mkdir -p $OUTPUT_DIR/{}"

 cat samples.list | parallel --jobs 1  "STAR --genomeDir $STAR_INDEX --twopassMode Basic --quantMode GeneCounts --readFilesCommand zcat --readFilesIn $INPUT_DIR/{}_1.fastq.gz $INPUT_DIR/{}_2.fastq.gz --outFileNamePrefix $OUTPUT_DIR/{}/{}. --runThreadN 20 --outSAMtype BAM SortedByCoordinate --sjdbGTFfile $GTF --outSAMunmapped Within  --outSAMattributes Standard --runMode alignReads"
	STAR_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/"
	INPUT_DIR="00_raw_fastq"
	OUTPUT_DIR="01_alignment_genes_count"
	GTF="/home/mRNAseq/ref/gencode/human/GRCh37.19/gtf/gencode.v19.annotation.gtf"
	RSEM_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/GRCh37.p13.genome"

	mkdir -p $OUTPUT_DIR

	cat samples.list \| parallel --jobs 1 "mkdir -p $OUTPUT_DIR/{}"

	cat samples.list \| parallel --jobs 1 "STAR --genomeDir $STAR_INDEX --twopassMode Basic --quantMode GeneCounts --readFilesCommand zcat --readFilesIn $INPUT_DIR/{}_1.fastq.gz $INPUT_DIR/{}_2.fastq.gz --outFileNamePrefix $OUTPUT_DIR/{}/{}. --runThreadN 20 --outSAMtype BAM SortedByCoordinate --sjdbGTFfile $GTF --outSAMunmapped Within --outSAMattributes Standard --runMode alignReads"