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Each lane of data was first evaluated with TopHat [ 20] to create a set of read-supported junctions.
Each lane of data was demultiplexed by index sequence and reads were combined from both lanes for each sample.
Our analysis of next generation sequencing was motivated by the rapidly converging cost of microarray analysis with a single lane of data from an Illumina 1 G sequencer.
We used only one lane of data for each strain for copy number analysis (NCBI Sequence Read Archive accessions SRX014130 and SRX014132).
The numbers of reads attributable to each index/sample are calculated as a percentage of the total number of sequence reads per lane of data.
Although the maximum CV is smaller for the data combined across 5 lanes, than for a single lane of data, the trend is still apparent.
Similar(52)
These faults are most apparent when combining multiple lanes of data in the post-processing phase.
With Illumina pair-end sequencing technology, a total of 8 "lanes" of data was produced.
Illumina data were separated by tag using FastX Barcode Splitter and concatenating the two lanes of data for each tag respectively.
Figure 4 shows the result for 14 lanes of data, consisting of 3 replicate lanes for each of the 2 "control" rats and 4 replicate lanes for each of the 2 "SNL" rats.
Before comparing the effect of additional lanes, the degree of correlation between the replicate lanes was analyzed to ensure that additional lanes of data would not introduce excessive variation.
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