use GaIIx or HIseq

[induivain]

Hi Seqanswers
first I say that I dont have more experience in this area.
Now my group is using for resequecing a GaIIX, but we have the possibility of using a Hiseq but is more expensive, my question is. The area to resequence is 1.5mb, with GAIIX have 50x of coverage, but some areas only 5x, You think that using Hiseq would improve coverage of the 5x? I know that I have more reads , but I'm no sure if i would have diferent reads.

We use SureSelectXt and run 84 samples per plate in the GaIIX , the idea is only run 84 samples in the Hiseq, and the same samples , the same preparation.

Thank you in advance

[swbarnes2]

Hi Seqanswers
first I say that I dont have more experience in this area.
Now my group is using for resequecing a GaIIX, but we have the possibility of using a Hiseq but is more expensive, my question is. The area to resequence is 1.5mb, with GAIIX have 50x of coverage, but some areas only 5x, You think that using Hiseq would improve coverage of the 5x? I know that I have more reads , but I'm no sure if i would have diferent reads.

We use SureSelectXt and run 84 samples per plate in the GaIIX , the idea is only run 84 samples in the Hiseq, and the same samples , the same preparation.

Thank you in advance

If you have low diversity of reads, that's a library problem, and you are right, that more reads won't necessarily help that.

In the long run, Illumina is probably going to put their effort into improving reagents and firmware and software for the HiSeq, (and MiSeq) and not the GAIIx. So quality will continue to improve, costs will go down on the Hiseq, not so much for the GAIIx.

When the HiSeq is being used at full capacity, it is cheaper per Mb than a GAIIx.