paired inforamtion to construct Scaffolds

Question

[midox]

Hello,

I want to know how to use read pairing information to order and orient contigs to produce scaffolds using the net, I did not understand the procedure.

Thanks

[midox]

any response?!! please

Answer 1

[Antonio R. Franco]

Look information about mate paired reads They contain long distance sequence information that can be used to order contigs and also to resolve some issues about repeated sequences

[midox]

We assumed that there are two contigs and two paired-end reads, the first read overlaps with the first contig and second read overlap with the second contig. To the join of the two contigs, how it's done? Thanks

[Antonio R. Franco]

Is not like you say. Both, the first read and the second of a paired-end fragment will eventually end in a same contig because assemblers know that both ends come from the same short DNA fragment.

The problem raises when you assemble. In the assembling, you join many different fragments with paired ends, but you always end with many different contigs with no relation one to the others if using second generation NGS

Then, is when either the mate-paired sequences come handy and useful

There are two types of paired data

• the truly paired end reads coming from both ends of a SHORT fragment.

• And the mate-paired reads coming from very long sequences that needs to be processed in a different way (LOOK Figs 6B and 6C of this document). Mate paired were designed to give you the power or organizing the contigs by order. For example. If you have two sequences coming from the same mate-paired fragment, and you know that both sequences are separated 5kb, you can find that the right sequence of the mate-paired frament align to contig #45, whereas the left sequence OF THE SAME MATE PAIRED fragment align to contig #80.

This only means one thing. Both sequences are separated 5kb, and you can set the two contigs (#45 and #80) in that order. By combining the information of many mate -paired framents you can end with many ordered contigs. Gaps are then filled with many N to substitute the lack of information present between contigs. The number of N you place depends upon the distance

[midox]

Thanks for your explanations.

So mate-paired reads are the solution to order contigs. and for orientation of contigs? How to change the orientationd contigs?

And how to obtain the mate-paired reads? I have just the paired end reads.

Thanks

[Antonio R. Franco]

Just read the document I mentioned and look for Fig 6B and 6Cd

And yes. mate paired reads order and orientate the contigs, and even resolve some issues about repeated sequences