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deeptools_ATAC
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#computeMatrix reference-point --scoreFileName /rds/user/cjr78/hpc-work/ATAC/macs2/merged_replicates/merged_1_2_3_treat_pileup_scaled.bw /rds/user/cjr78/hpc-work/ATAC/macs2/merged_replicates/merged_7_8_9_treat_pileup_scaled.bw /rds/user/cjr78/hpc-work/ATAC/macs2/merged_replicates/merged_10_11_12_treat_pileup.bw --regionsFileName /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open_activated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_activated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_closed_deactivated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_closed.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_deactivated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_stable.bed --outFileName Alluvial_plot_clusters_ATAC.npz -a 2500 -b 2500 --referencePoint center --samplesLabel "Fh1 fl/fl" "Fh1 -/- CL1" "Fh1 -/- CL19" --numberOfProcessors $SLURM_NTASKS --missingDataAsZero
#computeMatrix reference-point --scoreFileName /rds/user/cjr78/hpc-work/ChIP/H3K27ac/macs2/merged_replicates/no_spmr_keep_dups/scaled_1_2_3_merged.bw /rds/user/cjr78/hpc-work/ChIP/H3K27ac/macs2/merged_replicates/no_spmr_keep_dups/scaled_4_5_6_merged.bw /rds/user/cjr78/hpc-work/ChIP/H3K27ac/macs2/merged_replicates/no_spmr_keep_dups/scaled_7_8_9_merged.bw --regionsFileName /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open_activated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_activated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_closed_deactivated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_closed.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_deactivated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_stable.bed --outFileName Alluvial_plot_clusters_H3K27ac.npz -a 2500 -b 2500 --referencePoint center --samplesLabel "Fh1 fl/fl" "Fh1 -/- CL1" "Fh1 -/- CL19" --numberOfProcessors $SLURM_NTASKS --missingDataAsZero
#plotProfile --perGroup --plotHeight 7 --plotWidth 7 --numPlotsPerRow 3 --colors blue red orange -m Alluvial_plot_clusters_ATAC.npz -o Alluvial_plot_clusters_ATAC.pdf
#plotProfile --perGroup --plotHeight 7 --plotWidth 7 --numPlotsPerRow 3 --colors blue red orange -m Alluvial_plot_clusters_H3K27ac.npz -o Alluvial_plot_clusters_H3K27ac.pdf
#computeMatrix reference-point --scoreFileName /rds/user/cjr78/hpc-work/ATAC/macs2/merged_replicates/merged_1_2_3_treat_pileup_scaled.bw /rds/user/cjr78/hpc-work/ATAC/macs2/merged_replicates/merged_7_8_9_treat_pileup_scaled.bw --regionsFileName /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open_activated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_activated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_stable.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_closed.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_deactivated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_closed_deactivated.bed --outFileName Alluvial_plot_clusters_ATAC_final.npz -a 5000 -b 5000 --referencePoint center --samplesLabel "Fh1 fl/fl" "Fh1 -/- CL1" --numberOfProcessors $SLURM_NTASKS --missingDataAsZero
#computeMatrix reference-point --scoreFileName /rds/user/cjr78/hpc-work/ChIP/H3K27ac/macs2/merged_replicates/no_spmr_keep_dups/scaled_1_2_3_merged.bw /rds/user/cjr78/hpc-work/ChIP/H3K27ac/macs2/merged_replicates/no_spmr_keep_dups/scaled_4_5_6_merged.bw --regionsFileName /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open_activated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_activated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_stable.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_closed.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_deactivated.bed /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_closed_deactivated.bed --outFileName Alluvial_plot_clusters_H3K27ac_final.npz -a 5000 -b 5000 --referencePoint center --samplesLabel "Fh1 fl/fl" "Fh1 -/- CL1" --numberOfProcessors $SLURM_NTASKS --missingDataAsZero
#plotHeatmap -m Alluvial_plot_clusters_ATAC_final.npz -o Alluvial_plot_clusters_ATAC_final.svg --perGroup --colorMap Reds Reds Reds Greys Blues Blues Blues --whatToShow 'heatmap and colorbar' --heatmapWidth 2 --heatmapHeight 2