Hello,



I am trying to use DESeq for miRNA sequencing data. We have 2 replicates (treated and untreated) i.e. a total of 4 samples. However, we have only around 200K-300K reads mapping to known miRNAs. I know this number is probably small, but we would still like to check for differential expression. The default options seem to be too conservative in our condition (may be due to the low number of reads), so I think may be using the "fit-only" option might be better. Since, we have lower reads I am thinking of using "genefilter's shorth" to estimate the size factors.



I am trying these different options but am wondering what according to you could be the best options for usage in our case. I am aware of the potential noise in our data, but we still expect to see something significant which is being lost in all this noise. I hope my question makes sense. I would appreciate any help on this.



Kindly let me know if you have any questions.



Thanks,
Praful


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