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March 25, 2024 08:24
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| (...) | |
| > #### Occupancy Analysis #### | |
| > png("Clustering_Occupancy.png", width= 840, height = 840) | |
| > plot(DBsample, cexRow = 1.4, cexCol = 1.4) | |
| > dev.off() | |
| null device | |
| 1 | |
| > | |
| > write("DBA COUNT", stderr()) | |
| DBA COUNT | |
| > #### Affinity analysis #### | |
| > DBcount <- dba.count(DBsample, bParallel=FALSE) | |
| Computing summits... | |
| Sample: NFCORE/work/results//bwa/merged_replicate/LA_M.mRp.clN.sorted.bam125 | |
| Sample: NFCORE/work/results//bwa/merged_replicate/LV_F.mRp.clN.sorted.bam125 | |
| Sample: NFCORE/work/results//bwa/merged_replicate/LV_FETAL_F.mRp.clN.sorted.bam125 | |
| Sample: NFCORE/work/results//bwa/merged_replicate/LV_FETAL_M.mRp.clN.sorted.bam125 | |
| Sample: NFCORE/work/results//bwa/merged_replicate/LV_M.mRp.clN.sorted.bam125 | |
| Sample: NFCORE/work/results//bwa/merged_replicate/RA_F.mRp.clN.sorted.bam125 | |
| Sample: NFCORE/work/results//bwa/merged_replicate/RA_M.mRp.clN.sorted.bam125 | |
| Sample: NFCORE/work/results//bwa/merged_replicate/RV_F.mRp.clN.sorted.bam125 | |
| Sample: NFCORE/work/results//bwa/merged_replicate/RV_M.mRp.clN.sorted.bam125 | |
| Re-centering peaks... | |
| Sample: NFCORE/work/results//bwa/merged_replicate/LA_M.mRp.clN.sorted.bam125 | |
| Reads will be counted as Paired-end. | |
| 2046638 Killed |
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| sampleId Peaks PeakCaller bamReads Tissue Condition QC Factor Replicate | |
| LA_M NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/LA_M.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/LA_M.mRp.clN.sorted.bam LA M 1 WT 1 | |
| LV_F NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/LV_F.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/LV_F.mRp.clN.sorted.bam LV F 1 WT 1 | |
| LV_FETAL_F NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/LV_FETAL_F.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/LV_FETAL_F.mRp.clN.sorted.bam LV FETAL 1 WT 1 | |
| LV_FETAL_M NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/LV_FETAL_M.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/LV_FETAL_M.mRp.clN.sorted.bam LV FETAL 1 WT 1 | |
| LV_M NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/LV_M.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/LV_M.mRp.clN.sorted.bam LV M 1 WT 1 | |
| RA_F NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/RA_F.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/RA_F.mRp.clN.sorted.bam RA F 1 WT 1 | |
| RA_M NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/RA_M.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/RA_M.mRp.clN.sorted.bam RA M 1 WT 1 | |
| RV_F NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/RV_F.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/RV_F.mRp.clN.sorted.bam RV F 1 WT 1 | |
| RV_M NFCORE/work/results//bwa/merged_replicate/macs2/narrow_peak/RV_M.mRp.clN_peaks.narrowPeak narrow NFCORE/work/results//bwa/merged_replicate/RV_M.mRp.clN.sorted.bam RV M 1 WT 1 |
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| # https://support.bioconductor.org/p/9142410/ | |
| library(BiocParallel) | |
| register(SerialParam()) | |
| library(DiffBind) | |
| library(ggplot2) | |
| library(DESeq2) | |
| plotDiffBind <- "__OUTDIR__/plots/DiffBindPlots" | |
| dataDiffBind <- "__OUTDIR__/data/processed/DiffBind" | |
| plotDiffBindQC <- "__OUTDIR__/plots/DiffBindPlotsQC" | |
| dataDiffBindQC <- "__OUTDIR__/data/processed/DiffBindQC" | |
| dir.create(plotDiffBind,recursive = TRUE) | |
| dir.create(plotDiffBindQC,recursive = TRUE) | |
| dir.create(dataDiffBind,recursive = TRUE) | |
| dir.create(dataDiffBindQC,recursive = TRUE) | |
| #### init #### | |
| sample=read.csv("__SAMPLESHEET__",h=TRUE ,sep="\t", stringsAsFactor = FALSE) | |
| sample$Treatment = sample$QC | |
| sample$Treatment[sample$Treatment == 0] <- "QC_FALSE" | |
| sample$Treatment[sample$Treatment == 1] <- "QC_TRUE" | |
| head(sample) | |
| setwd(plotDiffBind) | |
| getwd() | |
| #### Create dba object #### | |
| dir.create("__OUTDIR__/plots/DiffBindPlots", recursive = TRUE) | |
| write("LOAD DBA", stderr()) | |
| DBsample <- dba(sampleSheet=sample) | |
| write("DBA IS LOADED", stderr()) | |
| # saveRDS(DBsample, file = plotDiffBind,"DBsample.rds")) | |
| #### Occupancy Analysis #### | |
| png("Clustering_Occupancy.png", width= 840, height = 840) | |
| plot(DBsample, cexRow = 1.4, cexCol = 1.4) | |
| dev.off() | |
| write("DBA COUNT", stderr()) | |
| #### Affinity analysis #### | |
| DBcount <- dba.count(DBsample, bParallel=FALSE) | |
| write("DBA COUNT DONE", stderr()) | |
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