nuada · August 29, 2015 14:03
diff --git a/phix_screen.sh b/phix_screen.sh
 #!/bin/bash

 DATA='/data/project'
 for sample in $(cd ${DATA}; ls -1 *.r1.fastq.gz | cut -d . -f 1); do
        bowtie2 -x /resources/phix/bowtie2/phix -1 ${DATA}/${sample}.r1.fastq.gz -2 ${DATA}/${sample}.r2.fastq.gz -S /dev/null --al-conc-gz phix-${sample}.r%.fastq.gz -p 4 2>&1 | tee -a phix.log
 done
	#!/bin/bash

	DATA='/data/project'
	for sample in $(cd ${DATA}; ls -1 *.r1.fastq.gz \| cut -d . -f 1); do
	bowtie2 -x /resources/phix/bowtie2/phix -1 ${DATA}/${sample}.r1.fastq.gz -2 ${DATA}/${sample}.r2.fastq.gz -S /dev/null --al-conc-gz phix-${sample}.r%.fastq.gz -p 4 2>&1 \| tee -a phix.log
	done
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