Question: combining RNAseq data from different platforms

Question

[shaymaa_s_elgaafary]

Dear all, I have may be a naiive question Would it be possible to combine RNA seq data from different sequencing platforms for instance Hiseq and nextseq? Many thanks

[Carlo Yague]

What is your goal ? Differential expression analysis ? Do you have some sample that were sequence with both platforms ? If you do, then it should be possible.

[shaymaa_s_elgaafary]

Many thanks for your reply. So what you meant is to combine equal number of samples from the two different platforms is the only solution correct??

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

No. Equal number is not required. But you need to have sufficient samples of both groups in both technologies.

Answer 1

[WouterDeCoster]

If you want to compare treatment A sequenced on NextSeq with controls sequenced on HiSeq: no. Not okay. You are comparing also the technical differences in this comparison, which definitely with NextSeq could be significant.

But it is possible if you want to combine data from e.g.:

• 5 samples treatment A and 5 samples control on NextSeq
• 10 samples treatment A and 10 samples control on HiSeq

In the latter case, when performing differential expression analysis you can specify in the model which sample was sequenced with which sequencer.