2.5 years ago by
iGenomes has the best reference annotation for this tool, but hg38 is not available yet. I personally do not know the ETA for hg38, but you could ask them.
If you really want to use hg38, some things to check for in the reference annotation for optimal use of the available functions in Cufflinks (and more importantly, for Cuffdiff):
- chromosome identifiers are an exact match between all inputs (ref genome, ref annotation, any other external resources)
- gene_id and transcript_id have distinct values in the attributes field
- p_id and tss_id exist in the attributes field
- optionally, gene_name exists in the attributes field
- no duplicated "ID" values between distinct entries in the attributes field
If you locate a good file, please consider sharing it on http://usegalaxy.org. You can also write back here and we can consider including it in a shared Data Library for everyone to access directly.
Best, Jen, Galaxy team