Using GOLDENPATH

5. cDNA / Transcriptome Sequencing Appendix : 5.4 Reference Type Auto Detection : 5.4.1 Using GOLDENPATH

5.4.1

Using GOLDENPATH

5.4.1.1

Genomic Reference

When the GOLDENPATH environment variable is in use, the reference should not be specified when a genomic (gDNA) reference type is being used. The software will automatically find the reference and annotation files in the GOLDENPATH directory structure. When using the GUI, use the default setting for the reference type (Auto). On the command line, do not use the –gref argument with setRef, runProject, or runMapping.

setRef hg18

5.4.1.2

When a transcriptome (cDNA) reference type is being used in conjunction with the GOLDENPATH environment variable, auto-detection of the reference type is not possible. You must use the –cref argument as an option to setRef, runProject or newbler or select the corresponding choice on the GUI.

setRef –cref hg18