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allenday/kannapedia process unpaired reads.bash

Created February 5, 2017 01:35
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kannapedia process unpaired reads.bash
for B in $(find * -size 0); do
C=${B/.bam/};
echo $C;
java -jar ~/bin/picard.jar FastqToSam F1=$(ls -1 ${C}_*R1*.fastq.gz) O=$C.bam SAMPLE_NAME=$C;
done
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