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!ls /Volumes/web/symbiodinium/Oly_MBD/Bismark/


    

    




zr1394_1_cleaned_all_bismark_bt2.bam
zr1394_1_cleaned_all_bismark_bt2_SE_report.txt
zr1394_1_cleaned_all_bismark_bt2_sorted.bam
zr1394_1_cleaned_all_bismark_bt2_sorted.bam.bai
zr1394_1_cleaned_all_bismark_bt2_sorted.sam

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%%bash
bedtools genomecov \
-ibam /Volumes/web/symbiodinium/Oly_MBD/Bismark/zr1394_1_cleaned_all_bismark_bt2.bam \
-bg | awk '$4 > 9' \
> /Volumes/web/symbiodinium/Oly_MBD/Bismark/sr_zr1394_1.bedgraph


    

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