You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hello,
I'm using the tool Control-FREEC to evaluate the CNVs in my data, but I have some doubts about the _CNVs file given in output.
According to the manual information, the CNVs file should have 9 columns of results, but my result only output seven columns.
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Error in if (class(resultks) == "try-error") return(list(statistic = NA, :
the condition has length > 1
Calls: KS
In addition: Warning message:
In ks.test.default(values, score(normals)) :
p-value will be approximate in the presence of ties
Execution halted
Pvalue couldn't be added in CNVs. How can I eliminate this error.
Thanks for your reply. : )
The text was updated successfully, but these errors were encountered:
Hello,
I'm using the tool Control-FREEC to evaluate the CNVs in my data, but I have some doubts about the _CNVs file given in output.
According to the manual information, the CNVs file should have 9 columns of results, but my result only output seven columns.
This is my configuration file and command line:
freec -conf freec_LPS4.txt -sample LPS4.bam
[general]
samtools = /data_center_01/home/hubihao/anaconda3/envs/NB/bin/samtools
bedtools = /data_center_01/home/hubihao/anaconda3/envs/NB/bin/bedtools
sambamba = /data_center_01/home/hubihao/anaconda3/envs/NB/bin/sambamba
chrLenFile = /data_center_01/home/hubihao/script/hg19_index/hg19_EBV_target.fasta.fai
ploidy = 2
maxThreads = 4
breakPointThreshold = .8
window = 50000
chrFiles = /data_center_01/home/hubihao/script/hg19_chr/
outputDir = /data_center_01/home/hubihao/project/Neuroblastoma/FREEC_analysis/
sex = XX
[sample]
#matefile = [samfile]
inputFormat = BAM
mateOrientation = 0
[BAF]
makePileup = /data_center_01/home/hubihao/project/Neuroblastoma/FREEC_test/hg19_snp142.SingleDiNucl.1based.bed
fastaFile = /data_center_01/home/hubihao/script/hg19_index/hg19_EBV_target.fasta
SNPfile = /data_center_01/home/hubihao/project/Neuroblastoma/FREEC_test/hg19_snp142.SingleDiNucl.1based.txt.gz
I looked up the previous issue, but I didn't find anything that needed to be adjusted in my config file, because I didn't have a control?
Also, I had some problems with the CNVs using assess_significance.R.
cat assess_significance.R | R --slave --args LPS4.bam_CNVs LPS4.bam_ratio.txt
And then this is the script's error message:
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
The following objects are masked from ‘package:base’:
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:base’:
Loading required package: IRanges
Loading required package: GenomeInfoDb
Error in if (class(resultks) == "try-error") return(list(statistic = NA, :
the condition has length > 1
Calls: KS
In addition: Warning message:
In ks.test.default(values, score(normals)) :
p-value will be approximate in the presence of ties
Execution halted
Pvalue couldn't be added in CNVs. How can I eliminate this error.
Thanks for your reply. : )
The text was updated successfully, but these errors were encountered: