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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:

Code Block
languagebash
titleRun bedtools multicov to count BAM alignments overlapping a set of genes
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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bedtools merge also requires that the input BED file be sorted by locus (chrom + start), so we do that first, then we request a strand-specific merge (-s):

Code Block
languagebash
titleUse bedtools merge to collapse overlapping gene annotations
cd $SCRATCH/core_ngs/bedtools
sort -k1,1 -k2,2n sc_genes.bed > sc_genes.sorted.bed
bedtools merge -i sc_genes.sorted.bed -s -c 4,4 -o count,collapse > merged.sc_genes.txt

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