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The potentiometric responses of both assemblies were then measured as a function of urea concentration using a home-made portable potentiostat.
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The individual assemblies were then merged using both Velvet and Oases to produce a single reference transcriptome.
The transcripts from the 6 assemblies were then pooled and re-assembled using CAP3 [ 39] to produce a meta-assembly.
The five SAGs Velvet assemblies were then merged and co-assembled using the de novo assembly algorithm implemented in Geneious (Biomatters Ltd ,Auckland NZ).
The assemblies were then concatenated and the pool of 138,954 transcripts was re-assembled using CAP3 [ 28].
For each sample (or pool), all (independently produced) partition assemblies were then concatenated.
Assemblies were then dialyzed against TBS to remove cholate and promote NLP self-assembly.
All these assemblies were then merged with Cuffmerge.
Reference and de novo assemblies were then concatenated.
These assemblies were then merged into a single assembly using the cuffmerge function from Cufflinks [ 60].
These assemblies were then merged together using the Cuffmerge utility [ 79], into a general transcriptome assembly.
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