Ginkgo

STEP 0 Upload your .bed files (We accept *.bed and *.bed.gz, max 1GB/file, min 3 cells)

Next step

View analysis later

Access your results later at the following address:

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chromchromStartchromEnd
chr1555485555533
chr1676584676632
chr1745136745184

If your mapped reads are saved in the file reads.bam:

bamToBed -i reads.bam > reads.bed

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:

bowtie2 -x hg19 -U reads.fastq -S reads.sam

If you have paired-end reads, use the following command instead:

bowtie2 -x hg19 -1 reads_r1.fastq -2 reads_r2.fastq -S reads.sam

Step 2
Convert reads.sam to reads.bam:

samtools view -Sb reads.sam -q 20 -o reads.bam

Step 3
Convert reads.bam to reads.bed:

bamToBed -i reads.bam > reads.bed