Repository navigation
bamCoverage with DNAse-seq shift #1415
Description
Hi,
I am trying to create a bigwig file using the bamCoverage function for DNAse-seq data and I wanted to check if my implementation is correct. For ATAC-seq I am doing this:
alignmentSieve \
--ATACshift \
--bam file.bam \
-o file.shifted.bam
and then
bamCoverage \
-b file.shifted.bam \
-o file.bw \
--binSize 1 \
--normalizeUsing CPM \
--outFileFormat bigwig
I think for DNAse-seq I will first have to do the shifts on a BED file and then call bamCoverage. I was thinking doing something like:
bedtools bamtobed -i file.bam \
| awk 'BEGIN{OFS="\t"}{
if ($6=="+") print $1,$2,$2+1,".",1,"+";
else print $1,$3,$3+1,".",1,"-";
}' \
| bedtools bedtobam -g file.chrom.sizes -i - > file.shifted.bam
then
samtools sort -o file.shifted.sorted.bam file.shifted.bam
samtools index file.shifted.sorted.bam
and lastly the same bamCoverage call
bamCoverage \
-b file.file.shifted.sorted.bam \
-o file.bw \
--binSize 1 \
--normalizeUsing CPM \
--outFileFormat bigwig
Am I missing something? I haven't found an awk command for DNAse-seq but I think the above should work? As an additional note all my data is paired end.
Also, this is the only issue I found with a similar(ish) question. Is using that offset flag equivalent to what I am doing?
Thanks in advance.
Activity