When I am using cufflinks in galaxy the option use reference annotation, when selecting use reference annotation as guide it shows no gtf data set available but in Tophat I have used hg19 as a reference genome...so how could I select this....And also after running tophat the files shows it still running and it has not converted in green colour and not showing BAM file format
The Tophat result datasets are still gray (queued) or yellow (executing)? This means the job is not completed yet. History and Dataset FAQs are here: https://galaxyproject.org/support/#datasets-and-histories
Reference annotation and a reference genome are two different inputs. Consider reviewing a RNA-seq tutorial to better understand the protocol and tool form usage: https://galaxyproject.org/learn/
Your reference genome is hg19 and natively indexed at https://usegalaxy.org (and many other Galaxy servers), so that can be directly chosen on the tool form to use the indexes on the server.
For the reference annotation, it should also be based on hg19, and in GTF format. This is loaded by you into the history, labeled with the datatype
gtf, and then that dataset selected on the tool form.
iGenomes is the preferred GTF. It has distinct gene_id and transcript_id values plus other attributes that these tools make use of: p_id, tss_id, and gene_name. Download the hg19 tar archive locally, unpack it, then upload just the genes.gtf file into your Galaxy history. Source: https://support.illumina.com/sequencing/sequencing_software/igenome.html
Hope this helps! Jen, Galaxy team