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module load bedtools
bedtools bamtofastq [OPTIONS] -i input.bam -fq output.fastq
more output.fastq

While it's useful to be able to look at the fastq file, many analyses will be easiest to perform in bed format.  Bed format is a simple tab delimited format that designates various properties about segments of the genome, defined by the chromosome, start coordinates and end coordinates.  Bedtools provides a simple utility to convert bam files over into bed files, termed bamtobed.

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