User: jinxinhao1988

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Posts by jinxinhao1988

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Error with plotting with target sequencing data
... Dear all, I use cn.mops to run CNV test in one sample without control. My data is Targeted sequencing data. It runs good until the plotting procedure. I use the command line as follows: > library(cn.mops) > BAMFiles <- list.files(pattern=".bam$") > segments <- read.table("targetRe ...
cn.mops written 21 months ago by jinxinhao19880 • updated 21 months ago by Günter Klambauer540
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Comment: C: Error when use getSegmentReadCountsFromBAM
... Thank you. Gunter. Problem has been solved. I generated a new reference with banner only have chrXXX. Best regards, ...
written 21 months ago by jinxinhao19880
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Comment: C: "genomdat must be numeric"error in DNAcopy Package
... Hi, After I change the "genomdat = cn[,6]" into "genomdat = as.numeric(cn[,6])" and "maploc = cn[,2]" into "maploc = as.numeric(cn[,2])". The problem has been solved. Thank you. ...
written 21 months ago by jinxinhao19880
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"genomdat must be numeric"error in DNAcopy Package (Solved)
... Hi, I am using Varscan2 to call CNV in tumor-normal samples. After the first two steps, an output.copynumber file and copynumber.called file have been generated.  Then I followed the protocol to use the DNAcopy package to do the CBS segmentation, My command line is as follows: library(DNAcopy) ...
dnacopy varscan written 21 months ago by jinxinhao19880
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Comment: C: Error when use getSegmentReadCountsFromBAM
... Hi, Gunter, Thank you for your reply. I use samtools to check the header of my bam files. It's like this. @HD     VN:1.0  SO:coordinate @SQ     SN:chr21_16510183_16510354_25   LN:172 @SQ     SN:chr19_42788849_42788989_CIC  LN:141 @SQ     SN:chr19_42790834_42790976_CIC  LN:143 @SQ     SN:chr19_4279 ...
written 21 months ago by jinxinhao19880
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Error when use getSegmentReadCountsFromBAM
... Dear all, I use cn.mops to call CNV in tumor-only samples, My data is Targeted DNA sequencing data. Preparations: I have prepared sorted bam file, bam index file and target region bed file. My bed file contains four columns(chromosome,start,end and name). Command lines are as follows: >libra ...
cn.mops targeted sequencing written 21 months ago by jinxinhao19880

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