Question: reference genome for miRNA sequencing
0
gravatar for F
2.6 years ago by
F3.4k
Iran
F3.4k wrote:

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???

mirna rna-seq • 717 views
ADD COMMENTlink modified 2.6 years ago by fusion.slope200 • written 2.6 years ago by F3.4k
1

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

ADD REPLYlink written 2.6 years ago by WouterDeCoster37k

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

ADD REPLYlink written 2.6 years ago by F3.4k
0
gravatar for fusion.slope
2.6 years ago by
fusion.slope200
fusion.slope200 wrote:

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

ADD COMMENTlink written 2.6 years ago by fusion.slope200
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