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cmdcolin/convert_bam_to_bigwig.sh

Last active September 25, 2015 22:20
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Convert BAM to bigwig (parallel)
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convert_bam_to_bigwig.sh
#!/bin/bash
samtools faidx reference_genome.fa
cut -f1,2 reference_genome.fa.fai > chrom.sizes
parallel "bedtools genomecov -ibam {} -g chrom.sizes -bg -split > {.}.bg" ::: *.bam;
parallel "bedGraphToBigWig {} chrom.sizes {.}.bw" ::: *.bg
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