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sub-task of #2
- [ ] 5a. human DLPFC ATAC-seq CP vs. VZ (Geschwind Cell 2018; ATAC-seq)
- [ ] 5b. ROADMAP fetal brain chromatin states
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I am running pipeline version: v1.9.2. My pipeline runs till atac.macs2_signal_track, then the next atac.qc_report is not triggered. I have following questions about the pipeline:
> 1. Is there …
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I installed the latest version of caper and the ATAC-seq pipeline, and the pipeline is stalled at the read_genome step. It has been running for multiple days without progress. I have been running it o…
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based on discussion with C today, I'm going to shift away from embedding SELEX-seq probes and towards embedding shorter windows of ATAC-seq peaks.
To that end, I need to do several things for the d…
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Hi,
first of all, thank you for providing a wonderful tool. I ran the ATAC-seq analysis using the pipeline on data as shown below
1. control -> no replicate
2. sample -> 2 biological replicate.
…
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Hello,
I am attempting to use MMARGE for analyzing ATAC-seq data from different strains of mice. I downloaded the SNP and Indel vcf files from the Mouse Genomes Project website and sorted them usin…
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Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines:
https://github.com/kundajelab/atac-seq-pipeline
https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P…
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I have installed snakepipes and downloaded ATACseq example for test run. However, the example does not run as I expected.
I first run following the suggestion from command.sh and get this:
#####
(s…
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This error occurs while using the atac-seq-pipeline but I do not believe this is specific to that. When using Singularity, relative paths to local input files do not get included in the Singularity bi…
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Hi,
Is there a plan to add a footprinting analysis module in atac so that it can visualize TF footprints like Signac and ArchR?
I am pretty interested in muon and it could be an alternative tool…