9 columns, chromosome, source, type, start,end, score, strand, score, name
chr22 TeleGene enhancer 10000000 10001000 500 + . touch1 chr22 TeleGene promoter 10010000 10010100 900 + . touch1 chr22 TeleGene promoter 10020000 10025000 800 - . touch2
Look for overlaps
# report the SNPs which overlap genes $ cd /shared/gen220/data_files/features/ $ bedtools intersect -a HEG4.SNPs.vcf -b rice_chr6.gff $ bedtools intersect -a HEG4.SNPs.vcf -b rice_chr6_genesonly.gff # report the same but print out the gene feature too - use the -wo option $ bedtools intersect -a HEG4.SNP.vcf -b rice_chr6.gff -wo # report the gene features which don't have SNPs
Can do the same thing as intersect but allows the features to be 'grown'.
Merge features that are nearby (or overlapping). Useful for NGS reads and merging coverage
"eports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file."
So calculate the coverage, by reads, of features
$ bedtools multicov -bams HEG4.tophat.bam -bed rice_chr6_genesonly.gff