- (cd $SRR;
- fastq-dump ${SRR}.sra;
- bwa mem -t ${CORES} $REF ${SRR}.fastq.gz | samtools view -b -o ${SRR}.bam;
- samtools sort ${SRR}.bam -o ${SRR}.sorted.bam -T temp
- cufflinks -p ${MAX_MEM} -G $GTF ${SRR}.sorted.bam;
- rm -f ${SRR}.fastq.gz ${SRR}.bam
+ (cd $FROM_SRR_SRR;
+ fastq-dump ${FROM_SRR_SRR}.sra;
+ bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;
+ samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
+ cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
+ rm -f ${FROM_SRR_SRR}.fastq.gz ${FROM_SRR_SRR}.bam