Question: Copy Number Aberration detection using Average coverage file
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gravatar for BioCanLyse
6 months ago by
BioCanLyse0
BioCanLyse0 wrote:

Dear All,

I have a question which has been bothering me. I have been given a .txt file containing : chromosome number, start, end, avg coverage, min coverage, max coverage, %bases below threshold, bases below threshold.

I have 5 files that will be used as our reference (population) and 4 unhealthy files (all same file format).

This is a file generated by SureCall software by Agilent. (PAIR END sequencing, custom panel NGS)

My task is to provide a list for each gene with the locations that have undergone copy number losses/gains. I am not sure how I can best normalise my data.. I have been told to take the mean of all the loci's avg coverage and compare that to each individual avgcoverage number although I feel that this is not appropriate as it does not take into account GC content bias and loci length..

I am able to utilise R. There are multiple packages available for it but I DO NOT have the raw fastq or BAM files..

Thank you for your help!!

ADD COMMENTlink modified 6 months ago • written 6 months ago by BioCanLyse0

Most of the copy-number alteration calling software accept the coverage files as input (just formatted in a nice way). I won't recommend my tool since it is designed for matched data, but this one http://bioconductor.org/packages/release/bioc/vignettes/PureCN/inst/doc/PureCN.pdf is exactly what you're looking for. Format your data in a suitable format and run the analysis!

ADD REPLYlink written 6 months ago by German.M.Demidov1.5k
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