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```
$ diff topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.ga topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.ga
$
```
@heylf do you have an idea which should be d…
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Dear,
Is it possible to use EPIC for cell type deconvolution using ATAC-seq datasets?
It gives the following error when I provide bulk ATAC-seq matrix (rows=peaks, columns=sample/subject) as inp…
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I am trying to call peaks in ATAC-seq data. According to the documentation:
> To find enriched cutting sites such as some DNAse-Seq datasets. In this case, all 5' ends of sequenced reads should be ex…
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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…
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Hi,
I understand that the default mapping option for the ATAC-seq data is pair ended, but is there a mapping option for a single ended ATAC-seq data?
Thank you,
Lindsay
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Hi,
Thanks for developing such an excellent tool for single-cell genomics. I am wondering whether you could provide the processing pipeline for Easysci-ATAC-seq.
Thanks.
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## **Invalid MEMLIMIT value with LSF on Linux**
When running the tutorial example for HPC with LSF, caper submits invalid memory unit format. Is lower case 'g' but should be 'G', resulting in the f…
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Hello,
I am trying to run the pipeline for chicken samples and have tried to create a custom genome reference for the pipeline. However, after finishing the steps here [https://github.com/ENCODE-de…
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Is there a way to run PePr without specifying input files, as is the case for analyzing ATAC-seq/DNase-seq data?