RNA-seq depth/plant

[Lucilia]

Hi everybody!
I'm a beginner in this subject and I have a doubt about the numbers of reads / coverage necessary for plant mRNA sequencing. I would like to sequence mRNA from apical meristems of a tree inoculated and non-inoculated with a pathogen, in order to identify the differential expression. No reference genome is available. I'm planning to perform 1x100 pb (illumina Hiseq) for each sample. According to the service provider they can guarantee 5-7.5 millions of reads per 10% channel. I wonder if it is enough for each sample. Where can I get some theoretical material about this issue? Thank you very much.

[upendra_35]

Ideally for doing DE you would need 10 million reads per replicate. However you can still do it with 5-7.5 million reads. I don't understand what do you mean by 10% channel. Could you explain that? Also without reference genome, how are you going to map your reads? Do you have closely related genome sequence available?

[pmiguel]

10% of a "channel" probably means 10% of a lane.

For a de novo transcriptome sequence you might want to use PE reads since they can aid in assembly.

--
Phillip

[Lucilia]

thanks puendra and Phillip.
I have a closely related genome available. The service provider used this term "10% per channel". I understood as Phillip explained.