Question

Basic4Cseq wiggle function

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ta_awwad ▴ 10

@ta_awwad-11382

Last seen 6 months ago

Frankfurt am Main

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 • 1.5k views

ADD COMMENT • link updated 3.5 years ago by koushik • 0 • written 5.8 years ago by ta_awwad ▴ 10

score 1 · Answer 1 · 2019-03-07

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Carolin Walter ▴ 10

@carolin-walter-7897

Last seen 7.5 years ago

Germany

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 COMMENT • link 5.8 years ago Carolin Walter ▴ 10

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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 REPLY • link 5.8 years ago ta_awwad ▴ 10

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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 REPLY • link 5.8 years ago Carolin Walter ▴ 10

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

ADD REPLY • link 5.8 years ago ta_awwad ▴ 10

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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")