Rat reference genome selection

[Danni]

Hi, I’m analysing my rat RNA, while when I was using featurecounts, I found there were so many reference genome to choose in USCS main browser. I’ve used ensemble genes as reference, which gave me only 40% assigned reads. I was wondering whether there is any good choice for rat reference genome?

For example, what’s the difference between these NCBI RefSeq tables?

[jennaj]

Combined into this topic Very low assigned reads in featureCounts