Hello Everyone,
I have a list of annotated meta genes in a bed file. I also have my chIP.bam and INPUT.bam files. How do I calculate the total length of basepairs lying within these genes that are enriched for my chIP?
Thank you for your support!
You would need to call peaks and then see how much they overlap (e.g., with bedtools intersect or bedtools coverage).
Hello Devon,
Thanks a lot for your reply. I m looking at a broadly distributed mark so I don't call peaks. I usually compute a log2ratio of fold enrichment over input and use this to define my regions. Is it correct to say that using bedtools coverage, if I sum up the total number of bp per gene that have a log2ratio >=1.0 for example, is my enriched genic length ?
Many thanks
Possibly, though I would encourage you to use a domain caller for broad marks rather than using a simple log2 ratio.
Hello Devon, Thank you for your reply. Would you have any suggestion of a suitable way to get a log2 ratio when the input has zero reads assigned? Assuming I have comparable coverage in both IP and Input, can I assign a pseudo count of +1 to these "zero reads" bins? my worry is that this would change the ratios significantly and affect my downstream calculations of gene length.
even if I use a domain caller, as you recommend, this problem still persists (I think)
Thanks again.
As you surmised, you need to add a pseudo-count. I think we default to 1 for this in deepTools, I haven't seen any better suggestion for that value.
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