[Bioperl-l] SeqIO: paired end reads

Lee Katz lskatz at gmail.com
Wed Aug 3 17:01:24 EDT 2011


Hi all!  I was wondering how to construct paired end reads from scratch.  I
know the locations of certain sequences across the genome with a high degree
of confidence and so I want to give them to my assembler as paired end
reads, along with my other sequence runs (454 and Illumina runs).  I plan to
use Newbler.

My only problem is that I do not know the correct format in order to specify
distance and sequences for a paired end reads run, and so I hope that there
is a SeqIO solution.  At the least, I hope that one bioperl member can point
me to where the definition of the paired end reads file format is...?

Thank you!

--Lee


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