paired-end reads mapped to genome.. gene with only one direction of paired-end reads?

[danwiththeplan]

I was hoping people would help me understand a weird situation I have encountered.

I have a genome assembly of a fungal genome (not done by me) which I have mapped raw RNAseq reads onto. RNAseq generally agrees quite well with predicted genes.

However in one gene that we are working on, the RNAseq agrees with the gene calls, but unlike other "genes" right next door on the same scaffold, all of the mapped reads are from one end of the paired end reads. The gene is big enough so that if one paired end read maps onto one end of the gene, the other one should logically be at the other end of the gene, which is the case in other genes next door.

Additionally, this weird gene has an identical copy right next door (this may be an assembly artefact)

Anyone have any idea what could cause this?

Genome assembled using velvet (I think.. not done by me) from multiple paired-end and mate-pair illumina runs.. transcriptome also from illumina runs.

[maubp]

It sounds like an assembly artefact in the area of this gene. Maybe there is some repeat structure in this region.

If you care about it enough, perhaps a little targeted capillary sequencing could resolve it?

[danwiththeplan]

thanks.. I am pretty sure it is a sequencing artefact on the genome, based on some wet work, but I still don't understand why only one direction of paired-end RNA reads map to these genes, but genes right next door have both directions of paired-end reads mapped to them successfully.