Paths to rerun [15/18]

All that is needed to do is to rerun the run_pipeline.sh in each directory

• /data/weirauchlab/project/vtr/EBV/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip/run2',
• /data/weirauchlab/project/vtr/EBV/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac
• [X] /data/weirauchlab/project/vtr/HPV_HPV16/Flp-In-TREx-HCT116/integrative_analysis/ChIP-seq/nf-encode-chip/run2
• [X] /data/weirauchlab/project/vtr/HPV_HPV16/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac,
• [X] /data/weirauchlab/project/vtr/HPV_HPV16/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip,
• [X] /data/weirauchlab/project/vtr/HPV_HPV16/Flp-In-TREx-HCT116/integrative_analysis/ATAC-seq/nf-encode-atac,
• [X] /data/weirauchlab/project/vtr/HPV_HPV18/Flp-In-TREx-HCT116/integrative_analysis/ATAC-seq/nf-encode-atac,
• [X] /data/weirauchlab/project/vtr/HPV_HPV18/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac,
• [X] /data/weirauchlab/project/vtr/HPV_HPV18/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip,
• [X] /data/weirauchlab/project/vtr/HPV_HPV6a/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac,
• [X] /data/weirauchlab/project/vtr/HPV_HPV6a/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip,
• [X] /data/weirauchlab/project/vtr/HPV_HPV11/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac,
• [X] /data/weirauchlab/project/vtr/HPV_HPV11/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip,
• [X] /data/weirauchlab/project/vtr/HPV_HPV6a/Flp-In-TREx-HCT116/integrative_analysis/ChIP-seq/nf-encode-chip,
• [-] /data/weirauchlab/project/vtr/HPV_HPV6a/Flp-In-TREx-HCT116/integrative_analysis/ATAC-seq/nf-encode-atac,
• [X] /data/weirauchlab/project/vtr/HPV_HPV11/Flp-In-TREx-HCT116/integrative_analysis/ATAC-seq/nf-encode-atac,
• [X] /data/weirauchlab/project/vtr/HPV_HPV18/Flp-In-TREx-HCT116/integrative_analysis/ChIP-seq/nf-encode-chip/run2
• [X] /data/weirauchlab/project/vtr/HPV_HPV11/Flp-In-TREx-HCT116/integrative_analysis/ChIP-seq/nf-encode-chip/run2

URLs

FLP-IN-293

HPV6a

• https://tf.cchmc.org/project/vtr/HPV_HPV6a/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac/analysis/multiqc/multiqc_report.html
• https://tf.cchmc.org/project/vtr/HPV_HPV6a/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip/analysis/multiqc/multiqc_report.html

HPV11

• https://tf.cchmc.org/project/vtr/HPV_HPV11/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac/analysis/multiqc/multiqc_report.html
• https://tf.cchmc.org/project/vtr/HPV_HPV11/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip/analysis/multiqc/multiqc_report.html

HPV16

• https://tf.cchmc.org/project/vtr/HPV_HPV16/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac/analysis/multiqc/multiqc_report.html
• https://tf.cchmc.org/project/vtr/HPV_HPV16/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip/analysis/multiqc/multiqc_report.html

HPV18

• https://tf.cchmc.org/project/vtr/HPV_HPV18/Flp-In-293/integrative_analysis/ATAC-seq/nf-encode-atac/analysis/multiqc/multiqc_report.html
• https://tf.cchmc.org/project/vtr/HPV_HPV18/Flp-In-293/integrative_analysis/ChIP-seq/nf-encode-chip/analysis/multiqc/multiqc_report.html

Flp-IN-TREx-HCT116

HPV6a

• (not finished running): https://tf.cchmc.org/project/vtr/HPV_HPV6a/Flp-In-TREx-HCT116/integrative_analysis/ChIP-seq/nf-encode-chip/analysis/multiqc/multiqc_report.html
• https://tf.cchmc.org/project/vtr/HPV_HPV6a/Flp-In-TREx-HCT116/integrative_analysis/ATAC-seq/nf-encode-atac/analysis/multiqc/multiqc_report.html

HPV11

• https://tf.cchmc.org/project/vtr/HPV_HPV11/Flp-In-TREx-HCT116/integrative_analysis/ATAC-seq/nf-encode-atac/analysis/multiqc/multiqc_report.html
  • Add readme explaining that failed was included in samplesheet but not to worry
• https://tf.cchmc.org/project/vtr/HPV_HPV11/Flp-In-TREx-HCT116/integrative_analysis/ChIP-seq/nf-encode-chip/run2/analysis/multiqc/multiqc_report.html

HPV16

• https://tf.cchmc.org/project/vtr/HPV_HPV16/Flp-In-TREx-HCT116/integrative_analysis/ChIP-seq/nf-encode-chip/run2/analysis/multiqc/multiqc_report.html
• https://tf.cchmc.org/project/vtr/HPV_HPV16/Flp-In-TREx-HCT116/integrative_analysis/ATAC-seq/nf-encode-atac/analysis/multiqc/multiqc_report.html

HPV18

• https://tf.cchmc.org/project/vtr/HPV_HPV18/Flp-In-TREx-HCT116/integrative_analysis/ChIP-seq/nf-encode-chip/run2/analysis/multiqc/multiqc_report.html
• https://tf.cchmc.org/project/vtr/HPV_HPV18/Flp-In-TREx-HCT116/integrative_analysis/ATAC-seq/nf-encode-atac/analysis/multiqc/multiqc_report.html

• Make sure this doesn't get chosen: HPV11-E6_E007908RepB
• Compare peak counts to previous