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Anna Battenhouse

Anna Battenhouse

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Here's how to run bedtools multicov, directing the standard output to a file:

Expand
titleSetup (if needed)
Code Block
languagebash
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* .
Code Block
languagebash
titleRun bedtools multicov to count BAM alignments overlapping a set of genes
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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