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2. GS Reference Mapper : 2.7 Customize Project with the Parameters Tab : 2.7.4 cDNA Project Input Sub-Tab
2.7.4
cDNA Project Input Sub-Tab
The cDNA Mapping project parameters on the Input sub-tab are the same as for Genomic mapping projects (Section 2.7.1) with the exceptions noted below.
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The NimbleGen sequence capture check box is not available.
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cDNA Mapping contains a section for specifying the Reference Type as cDNA, Genomic, or Auto (auto-detect).
Figure 59: gsMapper Parameters tab, Input sub-tab for cDNA projects
The reference type (cDNA or Genomic) can be automatically detected under certain circumstances, thus removing the need to specify the reference type on the command line. The logic employed depends on whether or not the GOLDENPATH environmental variable is in use. See Appendix 5.4 for more details.
The other two sub-tabs of the Parameters tab are identical for Genomic and cDNA projects.