Multiple NGS Platform and combining data

[Strider]

Hi all,

Would anyone care to comment on the validity of combining data from multiple platforms for a targeted resequencing project. In particular, I am looking at data from 454 and MiSeq for amplicon sequencing project. I am assuming the important things to look for are base calling quality, depth and coverage. If those are high quality then there should be no problem publishing the combined data sets?

Thanks

[JackieBadger]

Well both machine have different error profiles. So your error filtering protocols will most likely be different. For eg i found that systematic indel errors in 454 amplicon data could severely reduce the total depth of error free data, where MiSeq does not have the same issue. With the MiSeq we get much more depth so low copy number base mismatches, chimeras etc are much easier to distinguish compared to 454 data sets.
I imagine that after all is said and done and you have run each data set independently through the required QC stages, there is no reason why you can not combine the data