My favorite plant species has a 800 Mb genome and around 100 - 150 Mb transcriptom. It only has 15 genome assembly for 15 cultivars and several de novo RNA assembly. My cultivar has no existed genome assembly or transcriptom assembly. The published journal papers usually generates 50 Mb to 100 Mb reads per sample for de novo RNA assembly. I have a litmited budget.
So should I go shallow and generate 20 - 30 million reads per sample and do mapping using the existed genome assembly or transcriptom assembly of other cultivars? In this way, I can sequence more samples.
Should I go deep and generate above 50 Mb reads per sample an assemble my own transcriptom? In this way, I can only sequence fewer samples.
We are doing pilot experiments with limited budgets. My collaborator wants to have no replicate so that we can include more treatments. Is it a big no no? I personally prefer at least 3 biological replicates per each treatment.
Thank you so much for your kind help!