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broadinstitute / ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
MIT License
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More questions about code usage #45

Closed davidjohngreen closed 11 months ago

davidjohngreen commented 3 years ago

Hi there,

Many thanks for creating the tool - excellent work! I have a few questions about using it with my data.

I have ATAC-seq and H3K27ac ChIP-seq from three individuals (biological replicates).

I see that the tool allows replicates to be included, which is great. My question is - in this case, what is the best way to define the initial set of candidates?

I have three ATAC-seq files, and there might be small differences in the precise locations of peaks among individuals.

Is it acceptable to just use one of these ATAC-seq BAMs to define the candidates, and then put all of them into the tool as replicates? Or could I perhaps merge my three ATAC-seq BAM files and call MACS2 on this merged file to get an average location of the summits? Any help on this would be grealy appreciately.

David

engreitz commented 3 years ago

Hi David, Either of those two option (using one of the replicates, or merging them) would likely work fine, depending on the depth and reproducibility of the 3 replicate experiments Best, Jesse

On Sun, Dec 6, 2020 at 10:17 AM David Green notifications@github.com wrote:

Hi there,

Many thanks for creating the tool - excellent work! I have a few questions about using it with my data.

I have ATAC-seq and H3K27ac ChIP-seq from three individuals (biological replicates).

I see that the tool allows replicates to be included, which is great. My question is - in this case, what is the best way to define the initial set of candidates?

I have three ATAC-seq files, and there might be small differences in the precise locations of peaks among individuals.

Is it acceptable to just use one of these ATAC-seq BAMs to define the candidates, and then put all of them into the tool as replicates? Or could I perhaps merge my three ATAC-seq BAM files and call MACS2 on this merged file to get an average location of the summits? Any help on this would be grealy appreciately.

David

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-- Jesse Engreitz, PhD Assistant Professor, Department of Genetics BASE Research Initiative, Betty Irene Moore Children’s Heart Center Stanford University School of Medicine www.engreitzlab.org +1 (206) 310-3935