EXCAVATOR2tool Activity
Enhanced tool for detecting CNVs from whole-exome sequencing data
Status: Beta
Brought to you by:
albertomagi
Activity for EXCAVATOR2tool
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Livia Gozzellino created ticket #10
error during EXCAVATORDataAnalysis.pl
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YSK posted a comment on ticket #9
Dear Irene, I can't tell you about the best solution, but did you check this post? https://sourceforge.net/p/excavator2tool/tickets/1/ Please try to correct your bed file and rerun! :)
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Irene Ferraris posted a comment on ticket #9
Dear YSK, thank you for the tip. I have tried to change the EM algorithm in the LibraryFastCall.R as below: ############# EM Algorithm EMFastCall<-function(mdata,thru,thrd) { StartPar<-StartCond(mdata,thru,thrd) muvec<-StartPar$muvec sdvec<-StartPar$sdvec prior<-c(0.05,0.1,0.7,0.1,0.05) lvec<-c(-20,-1.3,-thrd,thru,0.9) uvec<-c(-1.3,-thrd,thru,0.9,20) LikeliNew<-sum(PosteriorP(mdata,muvec,sdvec,prior)*prior) threshold<-1e-05 for (i in 1:1000) { muvecold<-muvec LikeliOld<-LikeliNew taux<-EStep(mdata,muvec,sdvec,prior,lvec,uvec)...
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I have been struggling with the same problem for a very long time and may have finally solved it. Please note that this is an informal solution. Fix EXCAVATOR2/lib/R/LibraryFastCall.R. In the EM Algorithm, modify the part below "LikeliNew<-sum(PosteriorP(mdata,muvec,sdvec,prior)*prior)" as follows. Unnecessary parts are commented out. LikeliNew<-sum(PosteriorP(mdata,muvec,sdvec,prior)*prior) x = abs(LikeliNew-LikeliOld)-threshold if(is.na(x)) { x=FALSE }else { if(x<0) { break } } #if (abs(LikeliNew-LikeliOld)<threshold)...
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james posted a comment on ticket #9
I hava the exact same problem too. Have you solved the problem?
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Hi! I'm having the exact same problem. Running the analysis for several samples with the same kit and the same reference genome, some get the actual results while others don't. Thanks in advance for any response. Have a great day, Irene
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Vivian Chu posted a comment on ticket #1
Hi, I have a similar error to the one mentioned above. I merged the bed file using your command but after running it from scratch again, I also still get the same error with JointSeg.
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Adam Luo created ticket #9
EXCAVATOR2 EMFastCall Error
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gan shuang posted a comment on ticket #2
I got a similar problem like you but I do not understand how you solve it,can you share some specification? Thank you!
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JK Kim created ticket #8
How to run TargetPerla
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Emanuele Bosi posted a comment on ticket #7
Aaaand I put a typo in, it should be mkdir -p $Output_Folder/.tmp
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Improved portability across *nix ecosystem
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Lihi modified a comment on ticket #1
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Hello, I keep getting the same error eventhough I sorted the bed file as suggested above. any other suggestions? I ran it in paired mode. thx
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Hello, I keep getting the same error eventhough I sorted the bed file as suggested above. any other suggestions? I ran it in paired mode. thx
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Hello, I keep getting the same error eventhough I sorted the bed file as suggested above. any other suggestions? thx
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pradyumna J posted a comment on ticket #1
merge the overlaping bases with sort -k1,1 -k2,2n *.bed | bedtools merge
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This problem was solved by changing na.rm value from na.rm=T to na.rm=TRUE in the R scripts.
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Alessandro Gorohovski created ticket #6
A small example for the EXCAVATOR2 with results
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Problem in preparing analysis
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wenj.zhu modified a comment on ticket #4
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I only want to detect one specific CNV (about 16kb) locating in chr5:90159539-180687864 region. whole exome detection will take long time. So, I only put the exome interveals within chr5:90159539-180687864 into target.bed file and run TargetPerla.pl. But, it fails. So, I want to ask, target file shoule include whole exome interveals ?
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I only want to detect one specific CNV (about 16kb) locating in chr5:90159539-180687864 region. whole exome detection will take long time. So, I only put the exome interveals within chr5:90159539-180687864 into target.bed file and run TargetPerla.pl. But, it fails.
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step2: I can not find F4R.so file in EXCAVATOR2_Package_v1.1.2.tgz. Could you upload this file into EXCAVATOR2_Package_v1.1.2.tgz? EXCAVATOR2_Package_v1.1.2/lib/F77/F4R.so : cannot open shared object file: No such file or directory
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I only want to detect CNV in chr5:90159539-180687864 region, because we just focus on one deletion in this region. Maybe it is the reason why FilterTarget.R is wrong.
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Step one: perl /home/bin/software/EXCAVATOR2_Package_v1.1.2/TargetPerla.pl SourceTarget.txt target.bed test_w10000 10000 hg19
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problem of FilterTarget.R
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shahm3 created ticket #3
Mappability files
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Luka Topalovic posted a comment on ticket #2
Problem solved! Error was not setting sample name in path of output directory.
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Problem with DataAnalysis
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Alberto Magi posted a comment on ticket #1
Hi, this error comes when there's inconsistency with the target you have used. It's...
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Marc Pauper created ticket #1
Excavator2 module 3 error JointSegIn
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EXCAVATOR2tool released /EXCAVATOR2_Package_v1.1.2.tgz
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