I am looking for an established pipeline in GALAXY platform that I can use for the discovery/prediction of genes encoding for lncRNAs in the genome of the filamentous fungus Aspergillus nidulans; if not an established pipeline, are there any tools that I can potentially utilize in order to discover such genes encoding for such RNAs in the genome of Aspergillus nidulans?
Any help would be highly appreciated,
usegalaxy.* servers have 100s tools installed, and some can be used for lncRNA discovery. Maybe start with Google scholar and find a paper describing a similar analysis, the one you want to reproduce for A. nidulans. You can add “Galaxy” to query/search. You will need the reference genome and gene annotation. For annotation get both GTF and GFF formats. Get all files from the same server. NCBI is a good source of data. You probably will need repeat annotation as well, as some repeats can produce transcripts.
Hope this helps.