BOL

Merge overlapping bed file https://bedtools.readthedocs.io/en/latest/content/tools/merge.html #bed #merge #overlapping

make a window of 60k of bed file. $ bedtools makewindows -g genome -w 60000 > 60K.windows.bed #bed #bin #window

BAM2BED conversion bamToBed -i overall_exp_genome_rep1.bam > alignment.bed #Bed #bam #bamToBed #convert

Get the sequences using coordinates in bed file. $ bedtools getfasta -fi input_file.fa -bed regions_file.bed #Bed #Extract #Sequence #bedtools

Get the fasta sequence of the coordinates http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html #Fasta #Bed #Coordinates #Bedtools