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The main challenge with using this pipeline for ATAC-seq data is the use of STAR for mapping within the WASP subworkflow. We could create two new mapping rules within the WASP subworkflow that use `bo…
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Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure wa…
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Hi,
I have seen most papers doing ATAC-Seq analysis run macs2 with the --nolambda option, including the hmmratac paper. Naively, it seems like this would overcall peaks/peak summits in generally op…
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Hi Authors,
I am trying to reproduce the results of Fig3, I was able to run and finish almost all steps except
```
utils_GWAS.plot_enrichment_per_gene_linked_tiles_peaks([pbmc_ukbb_file], ukbb_f…
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**Use case**
My data consist of BAM paired-end files already filtered by duplicates, mit reads, etc. (99% alingment)
**Describe the problem**
I tried to use this command in bash
macs3 hmmratac…
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10x atac-seq data does not have UMI. Souporcell gives:
```
Traceback (most recent call last): File "/opt/souporcell/souporcell_pipeline.py", line 104, in assert float(num_umi) / float(num_read_te…
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Cell by bin
Visualize in higlass
Cell by peaks (in BED + snap files)
Annotated peaks (genomic intervals) per cell
Genome-wide (not necessarily tied to a gene)
Our Pipelines:
- [ ] We need to cre…
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#11
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Since epic2 is optimized for diffuse peaks (correct me if it is not), is it OK to run epic2 for narrow peaks, like regular TF ChIP-seq? I'm trying to find differential peaks for ATAC-seq, as I underst…
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pbmcs