comparison of Ion Proton RNAseq data with Illumina pair end data?

[vipul jain]

Hello everyone,

Can we compare Ion Proton RNAseq data with Illumina paired end data for expression analysis?

Thank you in advance.

[dpryan]

Well, you have to account for the batch effect of using different technologies. So if you sequenced group A on a HiSeq and group B on an ion torrent, then no the results wouldn't be easily comparable.

[sachin]

Well, you have to account for the batch effect of using different technologies. So if you sequenced group A on a HiSeq and group B on an ion torrent, then no the results wouldn't be easily comparable.

we have only case RNA-Seq data from Ion proton (not having control data set), please suggest how to do expressoin study..

[dpryan]

The simplest method woud be to sequence control samples with an Ion Proton too. While you can always try to use something like RUVseq, the results from any method like that will be necesarrily questionable.