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The back end data was prepared in MS Access 2000 (Microsoft Corporation Inc., USA).
The mate information for the paired end data was fixed by Picard.
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To this end data were collected in 2013/2014 from a tillage experiment established in 2005 as a randomized complete block design with two replications and three subplots on a Hyposodic Vertisol.
To that end, data is useful, if not completely definitive.
To this end, data were transformed for normality when necessary.
This is a reasonable approach when paired end data are available and we wish to trade off completeness for speed, but does result in decreased ability to detect insertions and deletions.
The 454 Titanium standard data and the 454 paired end data were assembled together with Newbler, version 2.3.
The 454 Titanium standard data and the 454 paired end data were assembled with Newbler, version 2.3.
We also used BreakDancer [ 23] followed by Pindel [ 24] to identify indels when paired end data were available.
Paired end data were mapped to the transgene sequences, and read pairs with only one end mapping to the transgene sequence were identified based on SAM flags.
To this end, data are usually transformed, and the appropriate transformation depends on the type of measurement (for microarray data, see Durbin et al. 2002).
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