uniqueome mappability file for EXCAVATOR-tool
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7.3 years ago
Canh • 0

Hi, I wish to use EXCAVATOR tool to detect Copy Number Variants (CNV) but this tool requires uniqueome mappability files. This page instructs to download these files from http://grimmond.imb.uq.edu.au/uniqueome/downloads/ but this link is no longer valid.

So, where else can I download these uniqueome mappability files? All the links I have found on the Internet seem to be invalid too.

Thanks in advance.

CNV • 3.0k views
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There is a new version, Excavator 2.

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Yeah, I've downloaded Excavator2 and it seems that the mappability files are provided within the Excavator2 package.

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Hi Canh,

Which directory did you find the uniqueome mappability files?

Are you referring to EXCAVATOR_Package_v1.1.2/data/ucsc.hg19.bw?

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7.0 years ago

Download EXCAVATOR2: https://sourceforge.net/projects/excavator2tool/ Unpack: tar zxvf EXCAVATOR2_Package_v1.1.2.tgz cd /path/to/EXCAVATOR2_Package_v1.1.2/ doc folder contains the manual --> read it; follow instructions for R/Samtools/Bedtools/Perl Go To /path/to/EXCAVATOR2_Package_v1.1.2/lib/F77/ Run: R CMD SHLIB F4R.f ; R CMD SHLIB FastJointSLMLibraryI.f --> This should be very smooth otherwise you have to download R source, untar the R package and inside (ex: cd R-3.3.1/ ) run: ./configure --enable-R-shlib=yes and if everything is OK type make.

Follow instructions in the manual: SourceTarget.txt should contain: /path/to/EXCAVATOR2_Package_v1.1.2/data/ucsc.hg19.bw /path/to/hg19.fa (space delimited) perl TargetPerla.pl SourceTarget.txt myTarget.bed MyTarget_w50K 50000 hg19

ExperimentalFilePrepare.w50K.txt should contain: /path/to/yourbamfile /path/to/output_bam samplename (space delimited) perl EXCAVATORDataPrepare.pl ExperimentalFilePrepare.w50K.txt --processors 6 --target MyTarget_w50K --assembly hg19

ExperimentalFileAnalysis.w50K.txt should contain (for cancer/paired mode otherwisw use T2...Tn for test samples and C1 for the control in case of population studies): T1 /path/to//EXCAVATOR2_Package_v1.1.2/Results_sample_test sample_test C1 /path/to//EXCAVATOR2_Package_v1.1.2/Results_sample_control sample_control perl EXCAVATORDataAnalysis.pl ExperimentalFileAnalysis.w50K.txt --processors 3 --target MyTarget_w50K --assembly hg19 --output /OutEXCAVATOR2/Results_MyProject_w50K --mode paired/pooling

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format your code with the 101010 icon in the writing tab for others to read it.

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6.1 years ago
xubeisi ▴ 30

I guess the bottom of http://www.imagenix.com/uniqueome/ could be used

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