genomeCoverageBed requires a sorted bowtieOut.sam
the following code worked for me:
Code:
samtools view -Sbo bowtieOut.bam bowtieOut.sam # convert to bam format samtools sort bowtieOut.bam sortedbowtieOut.bam # sort the bam file genomeCoverageBed -bg -ibam sortedbowtieOut.bam -g chrominfo.txt > out.bedgraph # compute coverage
-Lionel
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