chrom | chromStart | chromEnd |
---|---|---|
chr1 | 555485 | 555533 |
chr1 | 676584 | 676632 |
chr1 | 745136 | 745184 |
If your mapped reads are saved in the file reads.bam:
Step 1
If you do not have a reference genome index (e.g. hg19), download it from the Bowtie2 website (menu on right, under Indexes).
Then, map your reads (in reads.fastq) to the genome, and output the results to reads.sam:
If you have paired-end reads, use the following command instead:
Step 2
Convert reads.sam to reads.bam:
Step 3
Convert reads.bam to reads.bed: