How to check if reads are properly paired in mate-pair data?

[genepool_bee]

Dear all,

I have recently got some mate-pair data which has to be assembled denovo. Are there any ways through which we can determine if the reads are properly oriented and are at a distance expected before actually doing the denovo assembly.

Thanks for any ideas/suggestions.

[Linnea]

I suppose you don't have a close relative which you could map your reads on?

Do you have some paired end data? We assembled all paired end data first, and then mapped all mate pairs onto the paired-end denovo assembly. If the pair mapped FR with ins ~400bp, we discarded it as paired end contamination. Of course not all pairs will have both reads in the same contig, but you can at least get a proportion of "bad" pairs when comparing to the set mapping correctly (RF, with correct insert size).

I've also heard people done the same, but mapping to the mitochondrial genome (if you happen to have that).

Good luck!

[genepool_bee]

I suppose you don't have a close relative which you could map your reads on?

Do you have some paired end data? We assembled all paired end data first, and then mapped all mate pairs onto the paired-end denovo assembly. If the pair mapped FR with ins ~400bp, we discarded it as paired end contamination. Of course not all pairs will have both reads in the same contig, but you can at least get a proportion of "bad" pairs when comparing to the set mapping correctly (RF, with correct insert size).

I've also heard people done the same, but mapping to the mitochondrial genome (if you happen to have that).

Good luck!

Thank you very much for your reply. No, we haven't got any related reference, but yes we have paired end data. I will try to assemble them and map mate-pair reads to it..Thanks again for your suggestion.