Pseudogenes originate from gene duplications that have taken place through evolution. The homology between gene-pseudogene pairs can be as high as 100% and this can be a challenge when analyzing sequencing data. In some cases, reads exist that map equally well to the gene and it's pseudogene and this can be taken into consideration when analyzing the sequencing data. More specifically, a built-in functionality in the tool Trim Primers of Mapped Reads allows removal of reads that originate from a pseudogene but have been mapped to the target gene, if a gene-pseudogene track has been provided as input to the primer trim tool. Gene-pseudogene tracks are provided for some of the QIAseq gene panels. If you would like to provide your own list of gene-pseudogene pairs, this can be imported using the Import Gene-Pseudogene Table tool, which can be found in the Import menu.
This importer takes as input a TXT or TSV file containing gene and pseudogene information. The input file has the following format: The first column contains a gene name, and the second column is a comma separated list of pseudogene names, so that each line contains information about one link between a gene and one or several pseudogenes.
When importing a gene-pseudogene table, a gene track must also be selected. Names of genes in the gene track will be used for matching names in the input file. If a name of a gene or a pseudogene from the input is not found in the gene track that was used during import, you will get a warning that will list the names of the genes that could not be matched and thus are absent from the imported track.
The output is a track of linked gene-pseudogene features that can be saved in the Navigation area. The gene-pseudogene track can be used as input in the tool Trim Primers of Mapped Reads, but can only be used with the same reference genome as was used when importing the gene-pseudogene table.