I am doing RNA-seq data analysis. And this requires reference genome and annotation gtf file.
When i read papers, I found that they always integrate genome data and gtf file from different source (UCSC refSeq and ensemble), but there is little detail information about how to do it.
So my question is
1. how to integrate genome data(.fasta) from different sources(UCSC refSeq and ensemble)
2. how to integrate annotation data(.gtf) from different sources(UCSC refSeq and ensemble)