I used an external spike-in for my ChIP-Seq experiment. By manual inspection and from original data input, the spike-in proves valuable as normalization tool.
Now I want to implement this in NGS-Plot. I find the easiest way is to use the spike-in library size instead of original library size for each bam. So I made a .cnt file for each bam file containing the spike-in number.
How to include that in NGS-Plot workflow? As I understood it, .cnt file will be used if provided, but that does not happen for me.
How to change that?
Thanks for your help!
Hi Community.
I used an external spike-in for my ChIP-Seq experiment. By manual inspection and from original data input, the spike-in proves valuable as normalization tool.
Now I want to implement this in NGS-Plot. I find the easiest way is to use the spike-in library size instead of original library size for each bam. So I made a .cnt file for each bam file containing the spike-in number.
How to include that in NGS-Plot workflow? As I understood it, .cnt file will be used if provided, but that does not happen for me. How to change that? Thanks for your help!