Reads Orientation

[VNou]

Hello,

Can someone briefly tell me what orientation can have pair end reads?
Can the have all of the following orientation?
Forward Reverse, Forward Forward, Reverse Reverse, Reverse Forward?

Thanks a lot

[maubp]

In principle yes.

Roche 454 paired end reads are really same strand, but many tools flip one round to mimic the more common mixed strand pairing seen in Sanger and Illumina reads.

[VNou]

When its written that short jumping reads have the following orientation:

<------------ ------------> what does this mean?

I am making some test with Velvet.Velvet expect reads from different strands facing each other (like Sanger's) and with the orientation above i have to reverse complement both of them (they told me this). But if i reverse complement both of them the result wont be the same? Can someone explain me what happen if i reverse complement the reads with the above orientation.

Thanks a lot

[maubp]

Search for "paired end" and "mate pairs" for the two styles used with Illumina.