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?
<p>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&rsquo;t make a problem in our case. However, a paper showed that read length could be a confounding factor as below for your reference.</p>

<p><a href="http://bib.oxfordjournals.org/content/early/2015/03/30/bib.bbv017.full">Danielsson F, James T, Gomez-Cabrero D, Huss M (2015) Assessing the consistency of public human tissue RNA-seq data sets. Brief Bioinform.</a></p>
