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5. cDNA / Transcriptome Sequencing Appendix : 5.4 Reference Type Auto Detection : 5.4.2 Not Using GOLDENPATH
5.4.2
Not Using GOLDENPATH
5.4.2.1
Reference and Annotation Files Are in the Same Directory
In this case, the software will automatically detect the reference type based on the annotation file that is present in the directory where the reference file is located. The following rules apply:
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The presence of an annotation file named refGene.txt tells the software that the reference type is genomic (gDNA), irrespective of the presence of any other annotation files.
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The presence of an annotation file named refLink.txt tells the software that the reference type is transcriptome (cDNA), UNLESS an annotation file named refGene.txt is also present.
 
5.4.2.2
Reference and Annotation Files Are in Different Directories
In this case, you must specify the location of the annotation files by using the –annot option or the corresponding choice in the GUI. Specifying refLink.txt tells the software that the reference type is transcriptome (cDNA). Specifying refGene.txt tells the software that the reference type is genomic (gDNA).
 
5.4.2.3
Obtaining Annotations from the Reference File
In some cases, separate annotation files are not available, but annotation data is included in the header line(s) of the reference file. By default, the software will assume the reference type is genomic. However, if the annotation data contains the following name/value pair:
gene=geneName
the software will set the reference type to transcriptome (cDNA).
Some reference files (e.g., FlyBase) explicitly declare the type of the reference by including the name/value pair type=referenceType. In these cases, the software will set the reference type to transcriptome if the specified reference type matches the string mRNA. Any other value, or the absence of the key type in the annotation data, will result in the software setting the reference type to genomic.