How to isolate gene from a single chromosome RNA-seq experiment using R package?

Question

[guillaume.dachy]

Hi everyone

In a RNA Seq experiment where we put a transgene in mice cells, my gene of interest (that transgene) is on an "artificial" chromosome which contains only this gene. I'm trying desperately to isolate that chromosome from the data, using R package cummeRbund (DESeq2 and edgeR are options too...). Does someone has an idea how to do that trick ?

Thank you so much for helping me...

Cheers

Guillaume

[GenoMax]

What exactly do you mean by "isolate that chromosome from the data"? Are you looking to see if reads have aligned to that "chromosomes" or how many have aligned or something else? This information should be in your aligned files as long as you had created a "reference genome" that included this "artificial" chromosome.

Answer 1

[Designerpot]

Please post an example of the data you're looking at. As genomax2 says, what you're looking to do is possible to do directly on the level of your aligned files (.sam/.bam), or in R. But if we don't know exactly what you're trying to do, we can't tell you how to do it.