FPKM formula

[g781]

Hi everyone,

About the FPKM formula, should I use the total number of paired-end reads in the raw fastq file as a normalization term or use the total number of paired-end reads with good qualities ( MAPQ>20) as a normalization term?

Which one is usually used? The paper just mentioned the total number of reads. It seems to me the number is from raw fastq. But I would think the number of good quality paired-end reads sounds more reasonable. Can someone give me some suggestions?

Thanks.

[dfhdfh]

It should be the number of reads you use for alignment, etc. These should be the ones passing your quality criteria.

[g781]

Hi dfhdfh

Got it. Thank you very much.