This paper mentions that CNV-seq can be used on NGS data, does this mean that CNV-seq can be used on RNAseq data?
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059128
and CNVer paper , says that the software can be used on short mated reads from NGS, does this also imply that CNVer can be used on RNAseq?
http://compbio.cs.toronto.edu/CNVer/
Thank you very much
A.Colombo
Yes in their original paper, they explicitly say they have used aCGH. I also was under the impression that CNV can only be used on whole genome sequencing ... etc
But in the linked paper above titled "Comparative study..." on page 1 they write, " motivated by a comparative study of CNV detection methods based on aCGH technique, we conducted a comprehensive comparison of six representative CNV detection methods based on NGS under different sets of conditions."
I know that RNAseq is apart of NGS technology, so it is ambiguous as to which type of technology they are using under NGS ..
And then I get more confused with CNVer, which uses SHORT mated reads.... which I know RNAseq is comprised of.
However, I am not sure why RNAseq is not allowed, because it is not explicitly stated as disallowed. But I do know whole genome sequencing and aCGH are primarily used.
thank you very much again
AC
I believe they've meant the alternatives to aCGH that come from NGS, not whole bunch of NGS methods. It is not the length of reads which defines applicability here, but the starting material, which is RNA in case of RNA-Seq :)
Please note that you should add your replies as "comments" not "answers" to your questions.