Created
July 15, 2021 14:29
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| #!/bin/bash | |
| samtools view -b -f 4 $1 > $1.unmapped.bam | |
| samtools index $1.unmapped.bam | |
| java -Xmx8g -jar /opt/picard/picard-tools-current/picard.jar SamToFastq I=$1.unmapped.bam F=$1.unmapped.bam.fastq | |
| /home/ionadmin/bin/bbmap/reformat.sh in=$1.unmapped.bam.fastq out=$1.unmapped.bam.fastq.fasta | |
| gzip $1.unmapped.bam.fastq.fasta |
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