Illumina sequence reads

[sabrinaelias]

Hi all!
Is there anyway to understand from the reads of illumina pair end data that whether they are start to start and forward to forward face or start to end and forward to backward face?

An urgent reply will be really appreciated.
Thanks

[RockChalkJayhawk]

Hi all!
Is there anyway to understand from the reads of illumina pair end data that whether they are start to start and forward to forward face or start to end and forward to backward face?

An urgent reply will be really appreciated.
Thanks

That information would be in the SAM file. See section 2.2.2 for the flag field. This is how you know if it is aligned properly.

[pj_oz]

If I understand your question correctly, you're wanting to know what orientation to expect with Illumina pair-end reads. I believe this is dictated by the chemistry involved in the generation of pair-end and mate-pair libraries.

You should expect that a pair-end (ie. short-insert) library should have an orientation with the reads on opposite strands and oriented toward each other, so the end of the Read A is closer than the start of Read A to Read B. Illustrated below.

Pair-end library
Read A Read B
--------> <--------


Mate-pair libraries however have the reverse orientation to this, so the reads are still on opposite strands but oriented away from one another. The end of Read A is further away than the start of Read A from it's mate, Read B. Illustrated below.

Mate-pair library
Read A Read B
<-------------- --------------->

Can anyone else confirm my understanding of this? Does this answer your question sabrina?

[pj_oz]

apologies, the spaces were reformatted in that last post so it's a bit difficult to interpret the illustrations...

[maubp]

Wrapping with [ code ] tags helps for when you need fixed width fonts in a forum post.

[sabrinaelias]

thanks pj. it helped.

[spenthil]

Can anyone else confirm my understanding of this? Does this answer your question sabrina?

Torst confirms this: http://seqanswers.com/forums/showthread.php?t=5085
and this thread: http://seqanswers.com/forums/showthread.php?t=3214
(http://www.google.com/search?hl=en&q...nd+orientation)