Hello ATAC-seq pipeline,
Previously, we did the ATAC-seq analysis manually by trimming adapters (Adapterremoval), alignment (Bowtie2), QC (remove blacklist, duplicates, unmapped reads, mito genes…), peak calling (MACS2), and peak annotation (ChIPseeker).

Luckily, we found this amazing and easy-to-use ATAC-seq pipeline on nf-core. We tried this pipeline and it works super great.

However, we are confused with 2 issues:

1. The TSS heatmaps are inconsistent between our ChIPseeker results and nf-core ATAC-seq pipeline. In our hands, we can see heatmaps with signals, but the pipeline shows no signal at all. Which heatmap is right?
   

2. We found that the pipeline only calls broad peak, but ENCODE ATAC-seq pipeline calls narrow peak. Why does nf-core pipeline only call broad peak?
   

Thank you!
Best,
Yuanjian Huang