I apologize as I was unable to find the exact answer to my question browsing through earlier threads (thought it is probably out there). Please feel free to link me if you can.
I am looking to analyze 25 samples using methylminer and subsequent seq analyses. I have been quoted for single end and paired end , 100bp reads, and suggested to go between 20-50 million reads per sample. (obviously a wide scope quote!)
Would it be more effective to perform single end reads with more reads per sample if I am concerned about rare DMR between samples? Or should I do less reads and stick with paired end reads to be more confident in my mapping. I'm bran new to this tech, so from what I have read this is what I am understanding to be the tradeoff between physically more reads vs pairing when thinking on a budget (obviously more reads and paired end would be the ultimate right?)
Thanks for any comments (and please if you have time ask me to clear up my question if it doesn't make sense in its current form)
I am looking to analyze 25 samples using methylminer and subsequent seq analyses. I have been quoted for single end and paired end , 100bp reads, and suggested to go between 20-50 million reads per sample. (obviously a wide scope quote!)
Would it be more effective to perform single end reads with more reads per sample if I am concerned about rare DMR between samples? Or should I do less reads and stick with paired end reads to be more confident in my mapping. I'm bran new to this tech, so from what I have read this is what I am understanding to be the tradeoff between physically more reads vs pairing when thinking on a budget (obviously more reads and paired end would be the ultimate right?)
Thanks for any comments (and please if you have time ask me to clear up my question if it doesn't make sense in its current form)