Question: 200 vs 400 bp Ion Torrent
1
gravatar for biotech
4.3 years ago by
biotech540
United States
biotech540 wrote:

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?

 

 

rna-seq ion torrent • 1.4k views
ADD COMMENTlink modified 4.3 years ago by Danielk570 • written 4.3 years ago by biotech540
2
gravatar for Gary
4.3 years ago by
Gary450
Taiwan/Taichung/China Medical University Hospital
Gary450 wrote:

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.

ADD COMMENTlink written 4.3 years ago by Gary450
1
gravatar for Danielk
4.3 years ago by
Danielk570
Karolinska Institutet, Stockholm, Sweden
Danielk570 wrote:

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. 

ADD COMMENTlink written 4.3 years ago by Danielk570

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

ADD REPLYlink written 4.3 years ago by biotech540
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