Question: How many Mio reads are recommended for RNA-sequencing experiments in yeast?
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gravatar for JJ
8 weeks ago by
JJ390
JJ390 wrote:

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!

rna-seq • 159 views
ADD COMMENTlink modified 8 weeks ago by grant.hovhannisyan1.3k • written 8 weeks ago by JJ390
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gravatar for grant.hovhannisyan
8 weeks ago by
grant.hovhannisyan1.3k wrote:

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.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by grant.hovhannisyan1.3k

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

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by JJ390
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