Question: 1D ChIP-seq dimension from HiChip data
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gravatar for ra2967
11 months ago by
ra296720
ra296720 wrote:

Hello all,

I have HiChip data from h3k27ac. I have analyzed it with the tools that Homer has for His analysis and data looks good (even if the normalization shouldn't be exactly the same than for HiC experiments).

However, when I try to analyze my 1D H3K27ac ChIP dimension taking all the reads from my fast files, I don't see any enrichment. Does anyone know how this data can be mapped to obtain bigwigs, the typical ones, from the sequencing data? Is it possible? In the original paper, they do not show any 1D bigwig from the chipped data. In fact, they say that they call peaks, but they don't even show any bigwig/bedgraph of chipped peaks:

HiChIP ChIP Peak Calling

Dangling-end and self-ligation reads from the GM12878 Smc1a HiChIP HiC-Pro output were combined and processed to be compatible as a MACS2 BED file input. MACS2 was then run on the BED file using the no model and extsize 147 parameters and a FDR cutoff of 1%.

Can anyone help me?

Thanks,

Robert

ADD COMMENTlink written 11 months ago by ra296720

It is not possible to reproduce any of your issues as you do not show any code or data examples.

ADD REPLYlink written 11 months ago by ATpoint36k

My question would be more about theoretical issues with this analysis and pipelines to analyze it (if possible), rather a specific example.

ADD REPLYlink written 11 months ago by ra296720
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