Genome Analyzer Sequencing and Analysis Sample Clauses

Genome Analyzer Sequencing and Analysis. From each processed amplicon pool, a total of 6 pmol of the library were added to one lane of the Genome Analyzer (GA) flowcell (Illumina, San Diego, CA). Single-end sequencing for 26 cycles was performed on the GA using the Illumina protocols for cluster generation and sequencing-by-synthesis. GA image analysis and base-calling were performed, respectively, with the Firecrest and Bustard software packages from the Illumina GA Pipeline. Mapping was performed with the MAQ software package (Li et al. 2008), using the following mapping parameters: a maximum mismatch (-n) of 3, a mutation rate (-m) of 0.01, and a maximum sum of mismatching base qualities (-e) of 140. The short sequence reads were mapped to the FMR1 region of the human genome reference (NT_011681.15, g.3435700 to g.3475545). The reference sequence was modified at the following SNPs, where the minor allele is incorrectly included in the reference sequence: rs1270092, rs1270091, rs4824232, rs4824233, rs5904650, rs11342854, rs61419778, rs5904816, and rs68020458. The reference sequence was further altered by masking repeat elements with RepeatMasker.
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Related to Genome Analyzer Sequencing and Analysis

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