I'm now using the function getDiffExpression.pl from Homer with the count table generated from annotatePeaks.pl.
Here is my codes:
getDiffExpression.pl countTable.peaks.txt ND T2D T2D T2D T2D ND > diffOutput.txt
Here is the errors:
Argument "-319,filename1..." isn't numeric in addition (+) at /share/pkg/homer/4.9/install/bin/getDiffExpression.pl line 339, <IN> line 3. Argument "-281,filename2..." isn't numeric in addition (+) at /share/pkg/homer/4.9/install/bin/getDiffExpression.pl line 339, <IN> line 3. ... !!! Warnining - something likely failed during R execution. !!! R script that was used: ####### basic script for running DESeq (generated by HOMER) ######## library(DESeq2) #Read Data in countData <- read.delim("0.564077262607501.edgeR.in.data.txt") colData <- read.delim("0.564077262607501.edgeR.groups.data.txt") dds <- DESeqDataSetFromMatrix(countData, colData,design=~Treatment,tidy=TRUE) dds <- DESeq(dds) res <- results(dds,tidy=TRUE) write.table(res,file="0.564077262607501.edgeR.out.data.txt",sep="\t",row.names=FALSE) !!! R execution details: Loading required package: S4Vectors 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, as.vector, 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, unlist, unsplit Loading required package: IRanges Loading required package: GenomicRanges 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")'. Loading required package: Rcpp Loading required package: RcppArmadillo Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative Calls: DESeqDataSetFromMatrix -> DESeqDataSet Execution halted rm: cannot remove `0.564077262607501.edgeR.out.data.txt': No such file or directory
It's a part of my count table.
PeakID (cmd=annotatePeaks.pl tss hg38 -raw -p 30.bed 32.bed 33.bed 36.bed 37.bed 38.bed) Chr Start End Strand Not Used Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type 30.bed Distance to nearest Peak, Peak ID 32.bed Distance to nearest Peak, Peak ID 33.bed Distance to nearest Peak, Peak ID 36.bed Distance to nearest Peak, Peak ID 37.bed Distance to nearest Peak, Peak ID 38.bed Distance to nearest Peak, Peak ID NM_001281971 chr19_KI270921v1_alt 34995 38995 + 0 NA promoter-TSS (NM_001281971) promoter-TSS (NM_001281971) 0 NM_001281971 3809 Hs.654608 NM_012314 ENSG00000221957 KIR2DS4 CD158I|KIR-2DS4|KIR1D|KIR412|KKA3|NKAT-8|NKAT8 killer cell immunoglobulin like receptor, two Ig domains and short cytoplasmic tail 4 protein-coding NM_021107 chr19 38928954 38932954 + 0 NA promoter-TSS (NM_001145901) promoter-TSS (NM_001145901) 0 NM_021107 6183 Hs.411125 NM_021107 ENSG00000128626 MRPS12 MPR-S12|MT-RPS12|RPMS12|RPS12|RPSM12 mitochondrial ribosomal protein S12 protein-coding -319,filename1_peak_13298 -281,filename2_peak_12994 -361,filename3_peak_17889 -182,filename4_peak_16289 -295,filename5_peak_17638 -289,filename6_peak_18334
The command I use to generate count table:
annotatePeaks.pl tss hg38 -raw -p peak1 peak2 peak3 peak4 peak5 peak6 > countTable.peaks.txt
Does any one know how to solve the errors? Also, is the count table in the right format? Thanks!