I am trying to do RNA seq analysis using STAR and hg19 from UCSC. I notice that the GTF file of UCSC only contains UCSC ID but no gene symbol. Does anyone knows how to convert UCSC ID to gene symbol after I finish my analysis? I tried DAVID and HGNC but can't find any match.
Would you guys recommend to use GENCODE genome and GTF? While I also notice that in the GENCODE release 19, there are only genome sequence on all region and also GTF on all region. I want to focus on primary chromosome, so those scaffold may not be helpful. What if I use genome on all region while using the GTF only on primary chromosome? Will that cause some issues?
Also, is there any difference between hg19 from UCSC and from GENCODE?
Thanks a lot!