Question: Bam to BigWig loss of data at MACS peaks (nothing in the BigWig why?)
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gravatar for contreras.xavier
3 months ago by
contreras.xavier0 wrote:

Hi all,

We have some Chip-Seq data (from Human HeLa cells, 30 million reads) for our factor of interest. If I check my data on a genome browser at some of my peaks called by MACS, I can not see anything in the BigWig (this is totally empty) while I can clearly see the BAMs (they are enriched where there is a peak). Most peaks are OK, BAMs and BigWig show the peak. But I have this problem of empty BigWig for some of these peaks.

I thought BigWig was just a sort of "better" representaiton of BAMs density. Is there some sort of filter when converting from BAMs to BigWig that could explain this discrepancy?

thank you for your help, Xavier

bam bigwig peaks chip-seq • 172 views
ADD COMMENTlink modified 3 months ago by genomax52k • written 3 months ago by contreras.xavier0
1

Can you edit the question to describe what commands you used to generate the bigwig from the bam?

ADD REPLYlink written 3 months ago by Chris Miller20k

Hi thanks for your reply, I do not have access easily to the specifics of the commands. After talking more to different people who handle those files in my institute, it seems that Bams at these regions have a score of zero (but we're not sure why as the score of sequencing of individual bases are very good). And it appears that MACS (at least the way we implemented it) does not take into account the score of the Bam while the conversion to BigWig would take it into account so that is why we see peaks but nothing in BigWig. We're still wondering why the score is at zero for these Bams.

ADD REPLYlink written 3 months ago by contreras.xavier0

Sorry to say, but the things you say do not make sense to me. What do you mean by bam score? You really have to dig out the exact command lines that your analyst used, otherwise the problem cannot be reproduced. Commands are necessary for macs and for the tool that was used to get the browser tracks.

ADD REPLYlink written 12 weeks ago by ATpoint5.7k
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