Using Total Reads In In Refseq Genes To Calculate The Rpkm
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What do you want to compare and how and for which purpose?
I've modified my questions.
Why don't you use one of the many programs that does this? you have rseqc or cufflinks or any other. I think that N y the number of reads in the sample.
sometimes you may want to compare data from different library preparation, such as stranded or unstranded, polyA selected or not. Then the total reads you used to normalize is very important. As I think, add all reads up in your research object(eg. refseq genes) is better than using total mapping reads in a sample.
Hi Camelbbs. I'm adding this comment to all your questions: Please take some time, before you ask a question, to think more about your problems and most likely sources of answers (manuals, FAQs, Google!, etc.). When you ask a question, include some context, tell us why you ask that question, what result you need, etc. Most of your questions are vague, impossible to answer or you changed them following an answer because it became evident that it was not clear. Cheers.