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 This page instructs to download these files from http://grimmond.imb.uq.edu.au/uniqueome/downloads/ but this link is no longer valid.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.
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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I guess the bottom of http://www.imagenix.com/uniqueome/ could be used
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There is a new version, Excavator 2.
Yeah, I've downloaded Excavator2 and it seems that the mappability files are provided within the Excavator2 package.
Hi Canh,
Which directory did you find the uniqueome mappability files?
Are you referring to EXCAVATOR_Package_v1.1.2/data/ucsc.hg19.bw?