atacseq
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nf-core
ATAC-seq peak-calling and QC analysis pipeline
Hi, all. I'm on a Redhat machine, using podman profile. Trying out the atacseq pipeline. (editing my original) I saw the error when I ran this again: (start paste) >...
The input file [here](https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv) is deprecated update to something similar to [this](https://github.com/nf-core/atacseq/blob/dev/assets/test.csv).
I recently opened a GitHub issue for the nf-core chipseq pipeline. This potential problem applies to atacseq pipeline as well. The issue regards the choice of genome size specified with...
Fastqc and Trimgalore works perfectly. However I have not been able to proceed to bwa step, even after I upgraded from 22.04.0 version to 22.08.0-edge nextflow version. Here is the...
It would be great to include biotype analysis using featureCounts in this pipeline.
Hello! I am trying to run tests for nextflow atac seq, but they fail: `nextflow run nf-core/atacseq -profile test,docker` Output: N E X T F L O W ~ version...
Does the pipeline apply the standard +4/-5 offsets to aligned reads to account for the precise Tn5 binding site? I have not been able to find this in the documentation...
Hi, I am using this really nice pipeline on my dataset. I am using an in-house reference genome and currently with the conda profile (I know that singularity or docker...
Dear all, We had started to discuss this topic in Slack, but I decided to raise this issue so the comments won't get lost. In brief, you currently use the...
Hi there, We noticed that it would be very useful to have the genome annotation already loaded to the IGV session file that is generated by the pipeline. At the...