copy number variation

Question

[v27]

I want to detect copy number variation in fungi data (paired-end, Illumina data). The data is as following:2 sensitive 2 resistant strains 1 reference

Could someone suggest me a tool for detecting CNV.

[arta]

Did you see Copy Number Variation Tools question that was asked before ?

Answer 1

[Dattatray Mongad]

Just map the known genes on processed reads and note down the number of times they aligned. Use appropriate alignmnet parameters. You can use bowtie aligner. At last you will have number of times each gene aligned in both samples. Relatively, you can conclude on gene copy number variation, provided that the sequencing depth is same for both the samples.