What is the best resource for other RNA sequences if our aim is to omit Other RNA(if any) contaminants in RNA-Seq Data. This Query seems discussed in different threads, but currently looking for a summarized solution of all such.
a) Select all OtherRNAs from NCBI of higher taxonomy filter For ex if sample is plant: Generate OtherRNA db from NCBI all[filter] AND "green plants"[porgn] AND (biomol_trna[PROP] OR biomol_snorna[PROP] OR biomol_snrna[PROP] OR biomol_rrna[PROP] OR biomol_scrna[PROP] OR biomol_crna[PROP])
b) Generate RNA db from specialized databases like silva,greengenes etc. But I think many of them harbour only rRNA sequences.
c) rfam db
pardon if query is not clear / is irrelevant