Question: Basic4Cseq wiggle function
0
gravatar for ta_awwad
6 months ago by
ta_awwad10
Frankfurt am Main
ta_awwad10 wrote:

Dear All, I am currently using Basic4Cseq package to analyse my 4C data.. the analysis pipeline seems fine .. I used two "4-based" cutters to generate my library .. the following report summarise the analysis results:

> getReadDistribution(eData, useFragEnds = TRUE, outputName = "")
[1] "total reads: 121278275"
[1] "reads on the viewpoint chromosome: 86345883 (71.2% of total reads)"
[1] "reads in the viewpoint region: 30200101 (24.9% of total reads)"
[1] "covered fragment ends in the viewpoint region: 54.68%"

However, when I tried to export wiggle file fo IGV using printWigFile I got the following error message:

Error in fragEnds[, 1] : incorrect number of dimensions

does anyone have an idea to solve this? many many thanks

basic4cseq • 145 views
ADD COMMENTlink modified 6 months ago by Carolin Walter10 • written 6 months ago by ta_awwad10
Answer: Basic4Cseq wiggle function
1
gravatar for Carolin Walter
6 months ago by
Germany
Carolin Walter10 wrote:

Hi,

the read distribution looks good, so the data should be imported correctly. Could you please check what happens if you use exportVisualizationFragmentData with your data? The output should be a simple csv file with "chrom", "start", "end", and "reads". If that looks strange (as in "empty", or "no reads at all"), would you mind posting your workflow (omitting any experiment-specific details like the actual viewpoint position)?

Thanks, Carolin

ta_awwad [bioc] schrieb am 2019-03-07:

ADD COMMENTlink written 6 months ago by Carolin Walter10

Hi Carolin, I run already exportVisualizationFragmentData and the output looks quite good .. here is some lines:

chrom   start   end reads
chr4    57273055    57273145    0
chr4    57273153    57273452    144.972378606144
chr4    57273453    57273619    0.00824549986384618
chr4    57273775    57273972    0
chr4    57274185    57274384    0
chr4    57274582    57274657    0
chr4    57274658    57274734    8.33620036234849
ADD REPLYlink modified 6 months ago • written 6 months ago by ta_awwad10

Hi,

ok, did you mask the actual chromosome identifier in your output data, or does your original data indeed say "chr" (and not "chr1", or "chr12"...)? If it's the latter, this may be the reason for the wig export problem. Could you please check if the chromosome identifiers look "normal" when you try something like this: fragmentData = rawFragments(expData) head(fragmentData)

Best, Carolin

ta_awwad [bioc] schrieb am 2019-03-07:

ADD REPLYlink written 6 months ago by Carolin Walter10

Hi, I just Masked the chromosome number .. sorry for not mentioning that

ADD REPLYlink written 6 months ago by ta_awwad10

the pipeline used is:

libraryFile <- "/Volumes/4C_seq/MboI_MseI.csv"
bamFile <- "/Volumes/4C_seq/trimmed.bam"
Reads <- readGAlignments(bamFile)
pointsOfInterestFile <- "/Volumes/4C_seq/MyLocus.bed"
Points<-readPointsOfInterestFile(pointsOfInterestFile)
Data = Data4Cseq(viewpointChromosome = "chr4", viewpointInterval = c(37331705, 37332936),
                      readLength = 51, pointsOfInterest = Points, rawReads = Reads)
rawFragments(Data) <-readsToFragments(Data, libraryFile)
nearCisFragments(Data)<-chooseNearCisFragments(Data, regionCoordinates = c("from","to"))
nearCisFragments(Data)<-normalizeFragmentData(Data)

printWigFile(Data, wigFileName = "MyData.wig")
ADD REPLYlink modified 6 months ago • written 6 months ago by ta_awwad10
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