How to filter the raw data for RPKM calculation

Question

[gerrychang1985]

Hi everyone,

I'm going to do some gene expression analysis recently. I plan to de novo assembly the transcripts, and then calculate the RPKM. But I'm confused by the filtration of raw data. When dealing with DNA reads, I know the PCR-duplication should be filtered out, but when coming to RNA expression, should I keep them?

Please help, thank you.

Answer 1

[Istvan Albert]

I would recommend reading the post:

Should We Remove Duplicated Reads In Rna-Seq ?

[gerrychang1985]

That one's really helpful, thank you very much！