200 vs 400 bp Ion Torrent

Question

[biotech]

We sequenced two years ago two RNA samples using RNA-seq with 200 bp Ion Torrent kits. Now we need biological replicated for these two samples. The sequencing service offers now the possibility to get 200 or 400 bp.

​Do you think I should upgrade to 400 bp or stay with 200 bp in order to avoid technical variability?

Answer 1

[Gary]

We have a similar experience. We integrated 50 bp reads produced by Illumina HiSeq2000 and 75 bp reads produced by Illumina NextSeq500 in a chicken project. Fortunately, it didn’t make a problem in our case. However, a paper showed that read length could be a confounding factor as below for your reference.

Danielsson F, James T, Gomez-Cabrero D, Huss M (2015) Assessing the consistency of public human tissue RNA-seq data sets. Brief Bioinform.

Answer 2

[Danielk]

I almost get the vibe that you know the answer :)

If it's important to you that batch effects are kept minimal for comparability to older data, keep doing 200 bps.

[biotech]

Yes Danielk, I will be cautious, stick with 200 bp this time.