RNAseq recommendations / terms read pairs vs. reads for paired end experiments

Question

[JJ]

Hi,

Encode recommends 10 to 25M reads per sample but have used single end data. So that would mean 10 to 25M read pairs per sample for paired end experiments, right? I appreciate the advice.

Thanks!

Answer 1

[Mark]

The number of reads sequenced doesn't change between single vs paired end sequencing. In paired end you sequence both ends. So if the recommended is 10-25m, that can be single or paired end. Of course PE is the better option, and strandedness is even better, so is larger read size.

The recommendation changes whether you are doing DE, looking for novel transcripts etc etc