Reputation:
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New User
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Frankfurt am Main
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9 months, 1 week ago
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3 years, 3 months ago
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Comment: C: Basic4Cseq wiggle function
... Hi, I just Masked the chromosome number .. sorry for not mentioning that ...
written 9 months ago by ta_awwad10
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Comment: C: Basic4Cseq wiggle function
... 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 = ...
written 9 months ago by ta_awwad10
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Comment: C: Basic4Cseq wiggle function
... 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 ...
written 9 months ago by ta_awwad10
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... 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] ...
written 9 months ago by ta_awwad10 • updated 9 months ago by Carolin Walter10
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... Thanks much it was really stupid question ... now everything works fine ..thanks once more TA ...
written 16 months ago by ta_awwad10
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... I managed to get the interaction matrix .. in my case 878 X 878 .. also I prepared the Granges of the interaction bins (878 Grange) .. now when I am trying to construct HTCexp object gives me the following error message: Error in dimnamesGets(x, value) : invalid dimnames given for “dsyMatrix” o ...
written 17 months ago by ta_awwad10
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... Thanks much Nicolas for your quick reply .. it would be great if you implement these functions to be suitable to import several Hi-C output formats Best TA ...
written 17 months ago by ta_awwad10
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... Hello everyone, I am really new in visualising Hi-C data. Now I have normalized .cool files and I would like to visiualize it in R using HiTC package .. my .cool files are in the following format: chrom1 start1 end1 chrom2 start2 end2 count balanced chr18 10500000 1060 ...
written 17 months ago by ta_awwad10
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... I figured it out .. jus have to convert this bed format to gff3 and that it. ...
written 17 months ago by ta_awwad10
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... Hi everyone, I extracted new annotated gene features from IGV as bed file with this format: chr17 11049086 11051487 YourSeq 999.4911 - 11049086 11051487 . 2 1735,230, 0,2171, chr17 11044924 11051487 YourSeq 995.2607 - 11044924 11051487 . ...
written 17 months ago by ta_awwad10