200 vs 400 bp Ion Torrent
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?
2 answers
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.
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