About alignment rate of Dendrobium officinale (a plant) used RSEM software

Question

[wensulin93]

Hello, Guys!

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!

Answer 1

[Rogerio Ribeiro]

There could be a number of reasons. I would start to perform a QC on the data (check if adaptors were correctly removed; base quality etc). It would probably help if you posted the RSEM command you used (I have no experience with RSEM but other users might).

[wensulin93]

Thanks! I will try !