srividya22/Advanced bedtools usage

## Advanced bedtools usage
Links:
http://quinlanlab.org/tutorials/bedtools/bedtools.html

Use Case 1:  Given a.bam and b.regions.bed. how to get the parts of b.regions.bed that are not covered by a.bam?
Answer:
bedtools genomecov -ibam aln.bam -bga \
               | awk '$4==0' |
               | bedtools intersect -a regions -b - > foo

Option -bga	Report depth in BedGraph format, as above (i.e., -bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: “grep -w 0$” to the output.
	Links:
	http://quinlanlab.org/tutorials/bedtools/bedtools.html

	Use Case 1: Given a.bam and b.regions.bed. how to get the parts of b.regions.bed that are not covered by a.bam?
	Answer:
	bedtools genomecov -ibam aln.bam -bga \
	\| awk '$4==0' \|
	\| bedtools intersect -a regions -b - > foo

	Option -bga Report depth in BedGraph format, as above (i.e., -bg). However with this option, regions with zero coverage are also reported. This allows one to quickly extract all regions of a genome with 0 coverage by applying: “grep -w 0$” to the output.