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 desesperately 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 

You add the human gene as an extra sequence (i.e., extra chromosome) to the FASTA file defining the mouse genome. (You do this yourself using unix tools rather than using an R package. You need to be familiar with FASTA, which is a simple text format.) Then align the reads to the augmented genome using an up-to-date aligner such as Subread or STAR. For example, using the Rsubread package, you would run buildindex() to build the index from the FASTA file then subjunc() to align the reads.

You will also need to add the transgene to the GFF file containing gene annotation. In the simplest case you might define a gene with a single exon being the whole of the extra chromosome. This is just a matter of adding a line to a GFF data.frame or file.

Hi Guillaume 

I am struggling to understand the actual problem you have, but have a look at the 'QuasR' package (https://bioconductor.org/packages/release/bioc/html/QuasR.html). There you have the possibility to align the reads in addition to the genome to auxiliary targets (i.e. your artificial chromosome).

Regards, Hans-Rudolf