Recently I have got my RNA-seq data of a fungal species under several treatments. There are refseq files (fasta, gbff and bbs) available in NCBI, but the alignment/mapping rate is quite low (3-4%). So here I have several questions:
1.Based on NCBI refseq, there is no annotation file available. For the tools in Galaxy, I used fasta refseq file but what is the usage of the gbff and bbs files? Where can I download the annotation gtf file of this species?
2.I cannot understand the low mapping rate. Based on my boss, since there is little about the species under investigation and they are not the same isolates, RNA-seq mapping will be difficult. Is it possible explanation for the low mapping rate?
3.the most important question: How can I use galaxy to run RNA-seq analysis without refseq?