Sequencing/Capture problems

[LFM]

Has anyone experienced that the sequences generated after the capture are mostly those not included in the capture??
I have just looked at 1/10 individuals so far, but none of my selected genes have any reads mapping to the exons, in some cases there are some reads in the introns... I am thinking all my precious sequences are still stuck to the beads
Any thoughts?

[SeqAA]

Are you seeing very low target enrichment or no enrichment?

[LFM]

I am seeing reads spread all over the genome, including the Y chromosome in samples that are supposed to be female. When I zoom into one of my genes of interest, there are no reads mapped to that area or there might be some in the intronic regions, but no reads mapped to the exons which are the areas I targeted.

L.

[NextGenSeq]

The X and Y chromosomes have regions of homology. In our last whole exome capture we got about 150X coverage from a HiSeq lane.

You will always get some reads mapping to the genome since the capture efficiency is not 100%. You should also get high coverage in the flanking intron regions up to about 100 bp from the splice junction.

[GW_OK]

So it's almost like you did a reverse-capture. Which system did you use? Did you swap a wash aliquot with your captured DNA aliquot maybe?