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Here's how to run bedtools multicov, directing the standard output to a file:
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| mkdir -p $SCRATCH/core_ngs/bedtools
cd $SCRATCH/core_ngs/bedtools
cp $CORENGS/yeast_rna/*.gff .
cp $CORENGS/yeast_rna/sc_genes.bed* .
cp $CORENGS/yeast_rna/yeast_mrna.sort.filt.bam* . |
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| language | bash |
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| title | Run bedtools multicov to count BAM alignments overlapping a set of genes |
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cd $SCRATCH/core_ngs/bedtools
module load bedtools
bedtools multicov -s -bams yeast_mrna.sort.filt.bam \
-bed sc_genes.bed > yeast_mrna_gene_counts.bed |
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