Find 0 coverage in the bam file

cd /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/05.Clone_GFP
bedtools genomecov -ibam L80_clone_GFP_sorted.bam -bga > L80_clone_GFP_sorted.bedgraph





bedtools genomecov -ibam /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L51/04.Clone/L51_clone_sorted.bam -bga | cat | grep -w 0$ > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L51/04.Clone/L51_0Coverage.bedGraph

bedtools genomecov -ibam /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L67/04.Clone/L67_clone_sorted.bam -bga | cat | grep -w 0$ > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L67/04.Clone/L67_0Coverage.bedGraph

bedtools genomecov -ibam /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L74/04.Clone/L74_clone_sorted.bam -bga | cat | grep -w 0$ > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L74/04.Clone/L74_0Coverage.bedGraph

bedtools genomecov -ibam /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/04.Clone/L80_clone_sorted.bam -bga | cat | grep -w 0$ > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/04.Clone/L80_0Coverage.bedGraph


bedtools genomecov -ibam /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L51/05.Clone_GFP/L51_clone_GFP_sorted.bam -bga | cat | grep -w 0$ > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L51/05.Clone_GFP/L51_0Coverage.bedGraph

bedtools genomecov -ibam /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L67/05.Clone_GFP/L67_clone_GFP_sorted.bam -bga | cat | grep -w 0$ > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L67/05.Clone_GFP/L67_0Coverage.bedGraph

bedtools genomecov -ibam /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L74/05.Clone_GFP/L74_clone_GFP_sorted.bam -bga | cat | grep -w 0$ > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L74/05.Clone_GFP/L74_0Coverage.bedGraph

bedtools genomecov -ibam /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/05.Clone_GFP/L80_clone_GFP_sorted.bam -bga | cat | grep -w 0$ > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/L80/05.Clone_GFP/L80_0Coverage.bedGraph

 bedtools genomecov -ibam 2014_human_clone_sorted.bam -bga | cat | grep -w 0$ > 2014_0Coverage.bedGraph