Hi everyone,
I am preparing to do a ddRADseq study using a HiSeq 2000 to 1) look for local adaptation to an environmental gradient and 2) look for population structuring at neutral loci. My species (a frog) doesn't have a reference genome and is not very closely related to annotated Xenopus. Despite this, being able to align to the Xenopus genome is a goal.
Given my budget and the setup of the sequencing facility that I use, I have to choose between sequencing 480 individuals using 50bp SE reads or 384 individuals using 125bp PE reads. I will be running 96 individuals as a pilot study. If 50bp SE reads are sufficient to address my question, I'd rather use that approach so I can include more individuals/populations in the study.
My question is if I do the 125bp PE reads in the pilot study, is it possible to downsample the 125bp PE reads to simulate what results would have looked like if I had used the 50bp SE reads.
I appreciate any advice. Including any generally concerning read length and PE vs. SE for this type of study. Also, please let me know if more information would be helpful. Thanks!
I am preparing to do a ddRADseq study using a HiSeq 2000 to 1) look for local adaptation to an environmental gradient and 2) look for population structuring at neutral loci. My species (a frog) doesn't have a reference genome and is not very closely related to annotated Xenopus. Despite this, being able to align to the Xenopus genome is a goal.
Given my budget and the setup of the sequencing facility that I use, I have to choose between sequencing 480 individuals using 50bp SE reads or 384 individuals using 125bp PE reads. I will be running 96 individuals as a pilot study. If 50bp SE reads are sufficient to address my question, I'd rather use that approach so I can include more individuals/populations in the study.
My question is if I do the 125bp PE reads in the pilot study, is it possible to downsample the 125bp PE reads to simulate what results would have looked like if I had used the 50bp SE reads.
I appreciate any advice. Including any generally concerning read length and PE vs. SE for this type of study. Also, please let me know if more information would be helpful. Thanks!
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