This is my bed file for all the exon coordinates I want to take out all the exons of a given gene. Let say I have gene in chr 1 which starts from
chr1 11868 12227 so I want to parse out all the exons that comes in between
This is my small subset:
cat exon.bed | head -10 chr1 11868 12227 + exon chr1 11871 12227 + exon chr1 11873 12227 + exon chr1 12009 12057 + exon chr1 12178 12227 + exon chr1 12594 12721 + exon chr1 12612 12697 + exon chr1 12612 12721 + exon chr1 12612 12721 + exon chr1 12974 13052 + exon
How do I parse out?
I use mostly R and bit of shell script but I'm not sure if I can use R, may a few lines of perl or shell script can help me solve my problem.