I am doing a research about Dendrobium officinale (a plant specie) RNA-seq.
I downloaded this specie Genome files (.fna and .gtf, enter link description here) to construct the "index file" (By RSEM-prepare-reference).
And I was ready to analyze some datasets (enter link description here) for my resarch.
However, I used RSEM to cacaulte the expression rate of RNA-seq datasets but the alignment rates were very low for RNA-seq datasets:
20189357 reads; of these: 20189357 (100.00%) were paired; of these: 20163475 (99.87%) aligned concordantly 0 times 6047 (0.03%) aligned concordantly exactly 1 time 19835 (0.10%) aligned concordantly >1 times 0.13% overall alignment rate
I don't know why. Could anyone solve for me?! Thanks too much!