Question: (Closed) Missing IntervalFile.R in PureCN
gravatar for preetipankajakshanpillai
18 months ago by

Hello to all,

I am working with whole genome sequence data to call copy number variant. I want to use purity and ploidy aware copy number caller, so, I chose PureCN for this. I downloaded the PureCN package from the official website. Now to start working with my data, I need to generate a basic interval file from a BED file containing target coordinates and the command for this is:

$ export PURECN="/path/to/PureCN/extdata"

$ Rscript $PURECN/IntervalFile.R --infile baits_hg19.bed --fasta hg19.fa --outfile baits_hg19_gcgene.txt

When I run this command '$PURECN//IntervalFile.R': No such file or directory. Please help me with this issue. Also, I searched for this code manually in package folder, but I could not find any such code. Please, help.

Thanks in advance!

ADD COMMENTlink written 18 months ago by preetipankajakshanpillai0

Hello preetipankajakshanpillai!

We believe that this post does not fit the main topic of this site.

Not a Galaxy question. Please post at another forum that helps with line command usage of Bioinformatics tools.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
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