Question: bamCompare the result if 0
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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!

ADD COMMENTlinkeditmoderate 10 months ago HI • 0 • updated 10 months ago Devon Ryan 90k
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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 REPLYlinkeditmoderate 10 months ago
ATpoint
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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 COMMENTlinkeditmoderate 10 months ago Devon Ryan 90k

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