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Old 03-08-2015, 04:09 AM   #43
aeonsim
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Location: Belgium

Join Date: Jun 2011
Posts: 45
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Quote:
Originally Posted by fanli View Post
Hi all,

Just wanted to add our data as well - this was from an RNA-seq library and I don't have paired HiSeq data. Still, you can see some ambitious reporting of quality scores albeit not nearly as bad as what aeonsim showed.

We're hopefully going to run a v2 kit soon and I'll update with those stats when I get them!
I'd acctually say they're worse than what we had, considering your using PE80bp and the first 10 or so bases on the forward reads shows an average Quality score drop of ~10 on the Phred Scale (~30 to 20).

However our conculsion from our testing is that the NextSeq with V1 chemistry is ok for RNAseq as the reads still map fine and the coverage is high, it's however not suitable for variant calling especially when one is interested in de novo variants or low coverage. As a result it's only being used internally for RNAseq currently.

We will aparently get access to the V2 kits as soon as they're available to see if that fixes the issue.

Last edited by aeonsim; 03-08-2015 at 04:26 AM.
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