Is it ok to combine RR run and HO run data for downstream data analysis?

[weigrc]

Dear all

One of our projects needs PE50 sequencing.

With Illumine HiSeq 1500, one Rapid Run PE50 has been accomplished, but per sample sequencing data (~60% of total) is not sufficient. We are thinking to have more sequencing reads (~40% of total) by using High Output run PE100 then trim these reads to PE50 ones.

Is there any concern for combining such two types of PE50 sequencing reads together? Both RR and HO runs will share the same file setting as zipping output bcl files and bin Q scores.


Thank you thank you.
Wei

[GenoMax]

What kind of an experiment is this? It should be ok to trim the data per your proposal but you are likely throwing good data away.

[weigrc]

Just HO PE100 sequencing is the most common run type here, more cost effective as well. We need to get more sequencing reads for downstream data analysis. Thinking if there is any Bioinformatics concern on the combination of 2 sets of sequencing data? eg, Sample A using 100% of HO data, and Sample B using 70% of HO data + 30 % of RR data. Is it ok?

And I was told by Illumina that HO and RR sequencings have different chemistry. Has anyone compared the data between HO and RR??

Thanks,
Wei

[westerman]

As GenoMax asked, what type of experiment? Transcriptome? Assembly? etc. Also what organism -- highly characterized (e.g., human, mouse) -- or not characterizes (e.g., a fungus).

In general there should be no problems with combining the data sets. Trimming to 50 BPs does seem like a waste of good data but it does depend on your experiment.

[weigrc]

This project is for Reduced Representation Bisulfite Sequencing (RRBS).

I was thinking it should be no problem with combining RR PE50 and the HO PE50 (derived from HO PE100) data. But Illumina tech support told that "...though both HO and RR running on HiSeq but it shares different chemistry. If you just want to combine the data set and not care the downstream analysis, I think it should be fine...", which makes me hesitate doing this. Anyway, I'd do another run of RR PE50. Thanks for your suggestions.

Regards,
Wei