I've been working with human RNAseq data (Illumina single-end) with some success with standard use of the Tuxedo suite using the hg19 assembly as a guide. But now we are trying to work with paired-end Illumina data from some transgenic mice. There are several transgenes in the genomes of the mice (EGFP, Cre etc) and we don't want to lose the expression information from these transgenes however of course they are not in the mm9 or mm10 genome assemblies. What is the easiest way to maintain these genes in our analysis?
Thanks for any suggestions!
Thanks for any suggestions!
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