Hi
I would like to identify the copy number variants in the plant genome. I am using CNV-seq to identify the cnvs. I tried to execute the cnv-seq.pl script to find cnvs using below command
./cnv-seq.pl --test my.hits --ref IRGSP-1.0_genome.fasta --log2-threshold=0.6 --genome rice --genome-size=373245519 -p 0.001 --bigger-window 2.
The minimum window size for detecting log2<=-0.6 should be 3376.08047608453 window size to use is 6018.00667741671 x 2 = 12036 window size to be used: 12036 read 37398153 test reads, out of 37398153 lines read 0 ref reads, out of 6220779 lines write read-counts into file: my.hits-vs-IRGSP-1.0_genome.fasta.log2-0.6.pvalue-0.001.count R package cnv output: my.hits-vs-IRGSP-1.0_genome.fasta.log2-0.6.pvalue-0.001.minw-4.cnv Error in library(cnv) : there is no package called ‘cnv’ Execution halted
But i could not load the library(cnv). Can anyone help me to load the cnv script in R. I installed cnvtools but its not the exact package it requires.
Did you follow the manual on their page about the installation? If you did are you sure it is correctly installed ? You should have the R package cnv installed in your computer to work? Do in a R terminal install.packages("cnv") or try it on bioconductor
Thank you sir. I installed cnv package in R and its working now.