Hi, I have been working on finding pseudogenes from clarias magur genome assembly available in genbank which is assembled to scaffold level and not to chromosome level. There is also protein fasta file of the assembly in the Genbank. I want to find pseudogenes from this genome. I tried pseudopipe but it returns errror. For shiu pipeline, we need to extract intergenic regions from the genome to be used as input. I do not know what is the use of this step and how to extract intergenic regions from genome. Tblastn of intergenic regions and protein is done. The shiu's pipeline is also doing repeat masking of intergenic regions for which repeat libraries of magur is needed which is not available. Can I skip this step of repeat masking or is there any alternative way? I request your valuable comments on this issue.
