Question: bamCompare the result if 0
gravatar for HI
8 months ago by
HI0 wrote:

I am using bamCompare to normalize my Chip-seq data (antibody + input). The reference genome is bigger than 10G, and every chromosome size is bigger than 600M, I run the bamCompare for each chromosome seperately(because there is no big enough memory to do with the whole genome; SES normalization; binsize=50), when I check the results of bamCompare, I found that the log2 ratio in every chromosome site bigger than 538M is 0 (even if I set --region chr1:500000000:830000000), I didn't find any information on the official website, then what should I do with this? Or is there any other software to calculate log2 ratio? Thanks!

bamcompare chip-seq deeptools • 218 views
ADD COMMENTlink modified 8 months ago by Devon Ryan92k • written 8 months ago by HI0

What is the ultimate goal that you need these values for? There are for sure alternative approaches that will work. Did you try using the enrichment or significance scores from a peak caller such as MACS2 for your analysis?

ADD REPLYlink modified 8 months ago • written 8 months ago by ATpoint25k
gravatar for Devon Ryan
8 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

I recently replied to an identical question on the deepTools email list. To my knowledge bigWig files don't support chromosomes larger than ~538 megabases, so there's nothing deepTools can do about that.

ADD COMMENTlink written 8 months ago by Devon Ryan92k
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