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Probeset from the two Illumina platforms were mapped to a common probeset Id using a mapping file provided by Illumina.
The probes of the different microarray platforms were mapped by a perfect match of their sequences.
Reads from the Illumina and Ion Torrent platforms were mapped against the S. aureus USA300_FPR3757 reference using SMALT [ 9].
Sequences from microarray platforms were mapped to gene and transcript sequences in the BFGR database to provide expression data on the genes and transcripts within the BFGR.
For the whole genome sequencing data the 32 strains that were sequenced on Illumina platforms were mapped with BWA mem –M 0.7.5a [ 43].
Features from all platforms were mapped to HTR clusters and our analysis was restricted to those that mapped unambiguously to one HTR cluster.
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When multiple probes from one platform were mapped to one probe from the other platform, a one to one probe pair was randomly selected.
In our current study, approximately 80% of transcripts detected in the top100 of one platform were mapped within the top1000 of the competing platform.
Genomes sequenced on the SOLiD sequencing platform were mapped to the reference BN genome using BFAST-0.6.4e (Homer et al., 2009 ).
The 10 strains that were sequenced on SOLiD platform were mapped with BWA 0.5.9 aln -c -l 25 -k 2 -n 10 (the latest version to support color space).
Next, the code which will execute on the embedded platform is mapped on the architectural model by a compiler (see Section 4.5).
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