Regarding reads number for mapping

Question

[SHIRUI]

Hi dear guys

How can I determine the appropriate number of reads for mapping onto Mus musculus ref genome and as much as possible cover all transcripts completely

Thank you

[lieven.sterck]

though you question makes some sense, you will need to provide a bit more info on what you're planning to achieve, what input data you (might) have, .... things like that to get a meaningful & usable answer

Answer 1

[GenoMax]

https://knowledge.illumina.com/library-preparation/rna-library-prep/library-preparation-rna-library-prep-reference_material-list/000001243

Also see #5: https://web.genewiz.com/rna-seq-faq

This is a generic recommendation. If you are looking for subtle differences then you may need to sequence deeper (i.e. more reads) and also include more biological replicates.