Question: How to identify the loci producing differential small RNAs between two samples?
1
gravatar for biolab
4.4 years ago by
biolab1.2k
biolab1.2k wrote:

Hi, everyone,

I have small RNA-seq data avaliable for two samples (wt and mutant), each of which have three replicates. I mapped the small RNAs on genome, and next want to identify which transcripts produce significantly more small RNAs in wt relative to mutant. Do you think Cuffdiff, edgeR and DESeq are suitable for this job? Is it the same as mRNA-seq differential gene expression analysis?

Thank you very much for any of your suggestions or comments.

small rnas • 1.1k views
ADD COMMENTlink written 4.4 years ago by biolab1.2k
2
gravatar for Mo
4.4 years ago by
Mo920
/
Mo920 wrote:

@biolab I suggest DESeq2 because it was built for such analysis! since you have replicate , I do not see any problem , good luck

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Mo920
1

I guess you mean DESeq2?

ADD REPLYlink written 4.4 years ago by Sean Davis26k

Hi, Mo, Thank you very much.

ADD REPLYlink written 4.4 years ago by biolab1.2k
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