I was using the MAKER pipeline for gene prediction on my RNA-seq data and the pipeline worked fine. Now the output it generated is named like this:
>maker-contig-dpp-500-500-exonerate_est2genome-gene-0.0-mRNA-3 protein AED:0.24 eAED:0.24 QI:184|1|1|1|0|0|3|1049|588
As you can see its not possible to really see what gene/protein this might be. So is there an easy way to get some info for my predicted genes which existing ones they might be? Any existing program or script?
This has to be a common problem, so there have to be solutions available right?
Are you annotating a new genome? Look at a few papers doing that kind of work, the supplementary data is always nice. Read in particular Genome Biology. In the latest issue you get the Cheetah genome http://www.genomebiology.com/2015/16/1/277