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Hi,
I was wondering if adding the feature of shifting and splitting the reads after the alignment would be helpful.
A recent review on the approaches to analyze ATAC-seq data ([Yan et al., 2020]…
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**Project:**
Pseudo-WGS variant calling for common cell lines mining ENCODE and Roadmap Epigenomics data Recent progress in sequencing technologies have led to a massive production of epigenetic datas…
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Hello!
This might be an unusual request, but I have been attempting to use Salmon Alevin for mapping of **scATAC-seq data** (10X Genomics platform) and have a few questions on how to best do this (/w…
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I am trying to run `ldsc.py` to measure enrichment of GWAS risk variants in open chromatin regions of interest. I have generated the thinned `*.annot.gz` files for these regions and computed the LD sc…
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**Describe the bug**
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
at HMMR_ATAC.Main_HMMR_Driver.main(Main_HMMR_Driver.java:425)
**To Reproduce**
This error only show…
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Hollis (@wrighth) is working on 3d visualization tooling for networks.
He is looking for potential datasets so Shannon McWeeney sent him our way.
Attached is an example of the format would needs the…
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Hi @davek44
we have ATAC-seq data in different tissues and we want use the basenji to predict the activaty of snps. We wonder we put all the ATAC-seq in different tissues togother to the bsenji for…
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As proposed in #9 and raised in #18, we need a 'match' function that will give you Segmentation elements for a query region set.
It's relatively straightforward for an exact match, but if matches a…
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Share the papers that you've identified as relevant to our reproducibility discussion here. You do not need to note in this issue which ones fall into each category.
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Hi,
I have gone through the other two ATAC-seq issues. Accordingly, I tried one run with BAMPE and one without. here are the codes.
``macs2 callpeak -t raw/dH1f_1.bam -n dh1f_1.broad -g hs -q 0.05…