how can I choice the reference in paired-end-read

[huanggm]

hi,
I am a newbie,i have a question about paired-end-read.
if i use the paired-end-read method,i must have a reference genome,but where does it come from?Is it must paired with the smaple?

[dpryan]

hi,
I am a newbie,i have a question about paired-end-read.
if i use the paired-end-read method,i must have a reference genome,but where does it come from?Is it must paired with the smaple?

Unless you plan to do de-novo genome assembly, you'll need a reference genome. This is regardless of the type of reads. The reference genomes are made using a variety of technologies (next-gen sequencing, Sanger sequencing of BACs, etc.), but the particular smattering of technologies used to create the reference won't really matter to you*.

*In general, though I can think of exceptions to this. You would likely know if that applied to whatever you're working on.