How many Mio reads are recommended for RNA-sequencing experiments in yeast?

Question

[JJ]

Hi all,

For human 20-30 Mio reads per sample for DE analysis is recommended what I've read - which adds up to about 8 samples per lane for Illumina HiSeq.

However, what is your recommendation for yeast? It's obviously a lot smaller. Would 15 Mio reads per sample be reasonable? Any experience here?

Thank you very much!

Answer 1

[grant.hovhannisyan]

For doing DE analysis (on gene level!) with Candidas and Saccaromyces (genome size ~10-12 MB) we usually sequence 20-25 M reads, after mapping we usually get 90-95% of unique mapping, so the "effective" reads are around 17-20 mln (if you do trimming you also get rid of some data). If you only plan to do DE, you can go even lower, say 10-15 mln, but if you add a bit more you also can do some additional things, e.g. variant calling, allele-specific expression, etc.

EDIT: if you have enough money, I would invest money to perform as many replicates as possible, with minimum of 3 per condition. This is a very nice work comparing depth vs replicates. + some self-advertisement from the field of fungal transcriptomics.

[JJ]

I always try to go for more than 3 replicates. Thanks for your input.