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# ATAC-seq Astrocyte Workflow
<!-- TODO: Fill out intro (AS) -->
ATAC-seq is a bioinformatics best-practice analysis pipeline used for ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data analysis. It is built upon the ENCODE ATAC workflow written in workflow description language (wdl) and uses Nextflow to run in the astrocyte platform.
## Requirements
- The ATAC-seq Source workflow ['astrocyte-atac-source] (https://git.biohpc.swmed.edu/s219741/astrocyte-atac-source).
@@ -8,7 +8,9 @@ This repo is used to wrap the existing ATAC-seq pipeline listed below (Runner),
- The ATAC-seq Runner workflow, 'astrocyte-atac-runner] (https://git.biohpc.swmed.edu/s219741/astrocyte-atac-runner). This repo contains the original ATAC-seq pipeline developed by the ENCODE team.
## The ATAC-seq Runner workflow
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This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq. The pipeline can be run end-to-end, starting from raw FASTQ files all the way to peak calling and signal track generation using a single caper submit command. One can also start the pipeline from intermediate stages (for example, using alignment files as input). The pipeline supports both single-end and paired-end data as well as replicated or non-replicated datasets. The outputs produced by the pipeline include 1) formatted HTML reports that include quality control measures specifically designed for ATAC-seq and DNase-seq data, 2) analysis of reproducibility, 3) stringent and relaxed thresholding of peaks, 4) fold-enrichment and pvalue signal tracks.
On HPC, make sure that Caper's conf ~/.caper/default.conf is correctly configured to work with HPC. The following command will submit Caper as a leader job to SLURM with Singularity
`caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name ANY_GOOD_LEADER_JOB_NAME`