Everyone knows the formula for RPKM compuation: rpkm=10^9*C/NL,where C is the reads number of the transcript, L is the length of the transcript and N is the total reads number of the sample
However, in my RNA-seq analysis pipeline, I have three "N".
1. total reads number
2. number of reads which can be mapped to reference genome
3. number of reads which are the result after mappable reads filtering using repeatmask
how to select the total reads number N for RPKM computation? I find that using three "N" have totally different effect.
Thanks very much.
However, in my RNA-seq analysis pipeline, I have three "N".
1. total reads number
2. number of reads which can be mapped to reference genome
3. number of reads which are the result after mappable reads filtering using repeatmask
how to select the total reads number N for RPKM computation? I find that using three "N" have totally different effect.
Thanks very much.
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