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Old 04-13-2017, 07:01 PM   #1
s18692001
Junior Member
 
Location: Taipei

Join Date: Apr 2017
Posts: 1
Question Error Issue of DiffBind (Deseq2) R package

I'm now using DiffBind R package to conduct differential analysis for ATAC-seq dataset and general samples dataset sheet is enclosed "DiffBind_sheet.csv".
In this analysis, I want to compare each cell type in two conditions (ND v.s. T2D), so I divided the general sheet into enclosed sheets with different cell names (PBMC, Monocyte, CD8Tcell, CD4Tcell, Bcell) and put them into DiffBind analysis (script: diff.R, diff.sh); although I could run it in general sheet, I couldn't run it successfully in divided sheets. It shows: (enclosed diff.sh.e8513532)
"Error in `colnames<-`(`*tmp*`, value = c("Chr", "Start", "End", "Conc", :
'names' attribute [9] must be the same length as the vector [7]
Calls: dba.plotHeatmap -> pv.getPlotData -> pv.DBAreport -> colnames<-
Execution halted"
and
"Warning messages:
1: In bxp(list(stats = c(-1.12728066403382, 0.537157990329394, 1.46379186588061, :
some notches went outside hinges ('box'): maybe set notch=FALSE
2: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
cannot compute exact p-value with ties"


Do you have any advice in these error and warning?

Thanks!


diff.sh.e8513532
Code:
Loading required package: GenomicRanges
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


ATAC_30_Bcell Blood  ND  1 narrow
ATAC_38_Bcell Blood  ND  1 narrow
ATAC_32_Bcell Blood  T2D  1 narrow
ATAC_33_Bcell Blood  T2D  1 narrow
ATAC_36_Bcell Blood  T2D  1 narrow
ATAC_37_Bcell Blood  T2D  1 narrow
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Error in `colnames<-`(`*tmp*`, value = c("Chr", "Start", "End", "Conc",  : 
  'names' attribute [9] must be the same length as the vector [7]
Calls: dba.plotHeatmap -> pv.getPlotData -> pv.DBAreport -> colnames<-
Execution halted
Loading required package: GenomicRanges
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


ATAC_30_CD4Tcell Blood  ND  1 narrow
ATAC_32_CD4Tcell Blood  T2D  1 narrow
ATAC_36_CD4Tcell Blood  T2D  1 narrow
ATAC_37_CD4Tcell Blood  T2D  1 narrow
ATAC_38_CD4Tcell Blood  ND  1 narrow
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Error in `colnames<-`(`*tmp*`, value = c("Chr", "Start", "End", "Conc",  : 
  'names' attribute [9] must be the same length as the vector [7]
Calls: dba.plotHeatmap -> pv.getPlotData -> pv.DBAreport -> colnames<-
Execution halted
Loading required package: GenomicRanges
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


ATAC_30_CD8Tcell Blood  ND  1 narrow
ATAC_32_CD8Tcell Blood  T2D  1 narrow
ATAC_33_CD8Tcell Blood  T2D  1 narrow
ATAC_36_CD8Tcell Blood  T2D  1 narrow
ATAC_37_CD8Tcell Blood  T2D  1 narrow
ATAC_38_CD8Tcell Blood  ND  1 narrow
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Error in pv.getPlotData(DBA, attributes = attributes, contrast = contrast,  : 
  Unable to plot -- no sites within threshold
Calls: dba.plotHeatmap -> pv.getPlotData
Execution halted
Loading required package: GenomicRanges
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


ATAC_30_Monocyte Blood  ND  1 narrow
ATAC_32_Monocyte Blood  T2D  1 narrow
ATAC_33_Monocyte Blood  T2D  1 narrow
ATAC_36_Monocyte Blood  T2D  1 narrow
ATAC_37_Monocyte Blood  T2D  1 narrow
Warning message:
No contrasts added. Perhaps try more categories, or lower value for minMembers. 
Error in pv.DBA(DBA, method, bSubControl, bFullLibrarySize, bTagwise = bTagwise,  : 
  Unable to perform analysis: no contrasts specified.
Calls: dba.analyze -> pv.DBA
In addition: Warning message:
No contrasts added. Perhaps try more categories, or lower value for minMembers. 
Execution halted
Loading required package: GenomicRanges
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


ATAC_30_PBMC_CD3CD28_45hr Blood  ND  1 narrow
ATAC_32_PBMC_CD3CD28_45hr Blood  T2D  1 narrow
ATAC_33_PBMC_CD3CD28_45hr Blood  T2D  1 narrow
ATAC_36_PBMC_CD3CD28_45hr Blood  T2D  1 narrow
ATAC_37_PBMC_CD3CD28_45hr Blood  T2D  1 narrow
ATAC_38_PBMC_CD3CD28_45h Blood  ND  1 narrow
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning message:
Unable to perform PCA. Make sure there aren't fewer sites than there are samples. 
Warning messages:
1: In bxp(list(stats = c(3.76447355099267, 3.76447355099267, 6.56565468033949,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
2: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
  cannot compute exact p-value with ties
3: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
  cannot compute exact p-value with ties
4: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
  cannot compute exact p-value with ties
5: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
  cannot compute exact p-value with ties
Loading required package: GenomicRanges
Loading required package: methods
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


ATAC_30_Bcell Blood  ND  1 narrow
ATAC_30_CD4Tcell Blood  ND  1 narrow
ATAC_30_CD8Tcell Blood  ND  1 narrow
ATAC_30_Monocyte Blood  ND  1 narrow
ATAC_30_PBMC_CD3CD28_45hr Blood  ND  1 narrow
ATAC_32_Bcell Blood  T2D  1 narrow
ATAC_32_CD4Tcell Blood  T2D  1 narrow
ATAC_32_CD8Tcell Blood  T2D  1 narrow
ATAC_32_Monocyte Blood  T2D  1 narrow
ATAC_32_PBMC_CD3CD28_45hr Blood  T2D  1 narrow
ATAC_33_Bcell Blood  T2D  1 narrow
ATAC_33_CD8Tcell Blood  T2D  1 narrow
ATAC_33_Monocyte Blood  T2D  1 narrow
ATAC_33_PBMC_CD3CD28_45hr Blood  T2D  1 narrow
ATAC_36_Bcell Blood  T2D  1 narrow
ATAC_36_CD4Tcell Blood  T2D  1 narrow
ATAC_36_CD8Tcell Blood  T2D  1 narrow
ATAC_36_Monocyte Blood  T2D  1 narrow
ATAC_36_PBMC_CD3CD28_45hr Blood  T2D  1 narrow
ATAC_37_Bcell Blood  T2D  1 narrow
ATAC_37_CD4Tcell Blood  T2D  1 narrow
ATAC_37_CD8Tcell Blood  T2D  1 narrow
ATAC_37_Monocyte Blood  T2D  1 narrow
ATAC_37_PBMC_CD3CD28_45hr Blood  T2D  1 narrow
ATAC_38_Bcell Blood  ND  1 narrow
ATAC_38_CD4Tcell Blood  ND  1 narrow
ATAC_38_CD8Tcell Blood  ND  1 narrow
ATAC_38_PBMC_CD3CD28_45h Blood  ND  1 narrow
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning messages:
1: In bxp(list(stats = c(-1.12728066403382, 0.537157990329394, 1.46379186588061,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE
2: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
  cannot compute exact p-value with ties
3: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
  cannot compute exact p-value with ties
4: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
  cannot compute exact p-value with ties
5: In wilcox.test.default(toplot[[i]], toplot[[j]], paired = FALSE) :
  cannot compute exact p-value with ties
diff.R
Code:
#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
library(DiffBind)
setwd("/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/DiffBind")
#list.files()
#list.files("peaks")
ta <- dba(sampleSheet = basename(args[1]))
#ta <- dba(sampleSheet = "DiffBind_sheet.csv")
ta <- dba.count(ta)
ta = dba.contrast(ta, minMembers = 2, categories=DBA_CONDITION)   
ta = dba.analyze(ta, method=DBA_DESEQ2)   
#ta.DB = dba.report(ta, contrast=1, th=.001, method=DBA_DESEQ2, bCounts=TRUE)

fname = basename(args[1])

pdf(file=paste(fname, "_T2D_ATAC_Pval_0.001_plotDiffHeatMap.pdf", sep = "",collapse = NULL ))
dba.plotHeatmap(ta, contrast=1, correlations=FALSE, scale="row", th=.001)
dev.off()
diff.sh
Code:
#!/bin/bash -l
module load R/3.3.2
for filename in /restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/DiffBind/*_sheet.csv ; do
Rscript diff.R  "$filename"
done
DiffBind_general_sheet.csv
Code:
SampleID,Tissue,Condition,Replicate,bamReads,Peaks,PeakCaller
ATAC_30_Bcell,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_30_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_30_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_30_CD4Tcell,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_30_CD4Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_30_CD4Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_30_CD8Tcell,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_30_CD8Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_30_CD8Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_30_Monocyte,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_30_Monocyte.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_30_Monocyte.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_30_PBMC_CD3CD28_45hr,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_30_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_30_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_32_Bcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_32_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_32_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_32_CD4Tcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_32_CD4Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_32_CD4Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_32_CD8Tcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_32_CD8Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_32_CD8Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_32_Monocyte,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_32_Monocyte.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_32_Monocyte.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_32_PBMC_CD3CD28_45hr,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_32_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_32_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_33_Bcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_33_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_33_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_33_CD8Tcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_33_CD8Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_33_CD8Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_33_Monocyte,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_33_Monocyte.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_33_Monocyte.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_33_PBMC_CD3CD28_45hr,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_33_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_33_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_36_Bcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_36_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_36_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_36_CD4Tcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_36_CD4Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_36_CD4Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_36_CD8Tcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_36_CD8Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_36_CD8Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_36_Monocyte,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_36_Monocyte.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_36_Monocyte.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_36_PBMC_CD3CD28_45hr,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_36_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_36_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_37_Bcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_37_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_37_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_37_CD4Tcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_37_CD4Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_37_CD4Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_37_CD8Tcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_37_CD8Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_37_CD8Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_37_Monocyte,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_37_Monocyte.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_37_Monocyte.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_37_PBMC_CD3CD28_45hr,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_37_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_37_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_38_Bcell,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_38_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_38_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_38_CD4Tcell,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_38_CD4Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_38_CD4Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_38_CD8Tcell,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_38_CD8Tcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_38_CD8Tcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_38_PBMC_CD3CD28_45h,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_38_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_38_PBMC_CD3CD28_45hr.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
DiffBind_Bcell.csv
Code:
SampleID,Tissue,Condition,Replicate,bamReads,Peaks,PeakCaller
ATAC_30_Bcell,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_30_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_30_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_38_Bcell,Blood,ND,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_38_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_38_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_32_Bcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_32_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_32_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_33_Bcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_33_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_33_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_36_Bcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_36_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_36_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
ATAC_37_Bcell,Blood,T2D,1,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/4shift/ATAC_37_Bcell.sed.sorted.rmdup.trimmed.shifted.bam,/restricted/projectnb/chengcancer/Simon/project/T2D/ATAC-seq/5callPeaks/ATAC_37_Bcell.sed.sorted.rmdup.trimmed.shifted_peaks.narrowPeak.filteredBlack.bed,narrow
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atac-seq, chip-seq, deseq2, diffbind, error

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