reference genome for miRNA sequencing

Question

[zizigolu]

sorry,

for differential expression of miRNAs in an organism with tophat should I use the same fasta of reference genome existed for organism or reference for miRNAs of organism???

[WouterDeCoster]

Could you be more precise about the experimental design? You expressed a miRNA in another organism?

[zizigolu]

thank you

I am working with recently sequenced smallRNA data from the pathogen fungi Aspergillus fumigatus and Candida albicans. my mentor is interested in the differential expression of miRNAs in response to human blood infection. Therefor I was given 2 replicates for each of the RNA-Seq experiments of both fungi and after their extraction from infected human blood: namely Af_1, Af_2, Ca_1, Ca_2 and HsAf-Af_1, HsAf-Af_1, HsCa-Ca_1, HsCa-Ca_2.

but I got confused about which reference genome or GTF file I need

Answer 1

[fusion.slope]

I think if you use only the genome reference with only miRNAs annotation you would bias your analysis...