Dear All, I am currently using the Basic4Cseq package to analyze my 4C data.. the analysis pipeline seems fine.. I used two "4-based" cutters to generate my library and my goal to generate a wig file to find trans interactions and further downstream analysis.. the following is the pipeline I used
## Bam to Wig using Basic4Cseq library(Basic4Cseq) library(BSgenome.Hsapiens.UCSC.hg19) createVirtualFragmentLibrary(chosenGenome = Hsapiens, firstCutter = "gatc", secondCutter = "ctag", readLength = 75, libraryName = "human_DpnII_Bfal.csv") library(GenomicAlignments) ## MCF7 libraryFile <- file.path("human_DpnII_Bfal.csv") bamfile <- file.path("MCF7-DB.bam") mcf7reads <- readGAlignments(bamfile) ### path to bam file mcf7reads pointsOfInterestFile <- file.path("demo_hg19.bed.txt") liverPoints<-readPointsOfInterestFile(pointsOfInterestFile) liverPoints l3mbtl3Data <- Data4Cseq(viewpointChromosome = "chr11", viewpointInterval = c(61908390, 61908490), readLength = 75, pointsOfInterest = liverPoints, rawReads = mcf7reads) l3mbtl3Data rawFragments(l3mbtl3Data) <- readsToFragments(l3mbtl3Data, libraryFile) l3mbtl3Data # normalization of near-cis data nearCisFragments(l3mbtl3Data) <- normalizeFragmentData(l3mbtl3Data) head(nearCisFragments(l3mbtl3Data)) getReadDistribution(l3mbtl3Data, useFragEnds = TRUE, outputName = "") printWigFile(l3mbtl3Data, wigFileName = "MCF7_DB_basic4cseq.wig")
the following report summarise the analysis results:
>getReadDistribution(l3mbtl3Data, useFragEnds = TRUE, outputName = "")  "total reads: 6462494"  "reads on the viewpoint chromosome: 4109392 (63.59% of total reads)"  "reads in the viewpoint region: 3517037 (54.42% of total reads)"  "covered fragment ends in the viewpoint region: 82.7%"
But while implementing
> printWigFile(l3mbtl3Data, wigFileName = "MCF7_DB_basic4cseq.wig")
getting an error
Error in fragEnds[, 1] : incorrect number of dimensions
The same pipeline code worked for some other samples with the same format/file type but getting the above error while dealing with others. Can anyone please have any idea how to solve this?