miRDeep2 out put

Question

[H-K]

Hi. Again me. I used miRDeep2 for identification of known and novel miRNAs. Software output was:

#miRNA, read_count, precursor,  total,  seq and **seq(norm)**

Is seq(norm), normalized read count? or TPM? What is differences between TPM and seq(norm)? Can I use seq(norm) for DESeq2 while I have no biological or technical replicates? Thanks.

Answer 1

[Buffo]

is normalized read count, TPM is dependent to transcript lenght and from miRNA-seq you don´t have it, you cannt use it. At least you are looking for precursos more than mature mirnas and perform the assembly.

[Kevin Blighe]

Hi Buffo, I moved your comment to an answer, as you are correct about the seq(norm) column.

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Can I use seq(norm) for DESeq2 while I have no biological or technical replicates?

As it's normalised counts, as stated by Buffoo, then you should not use it for DESeq2. DESeq2 will expect raw un-normalised counts.

Take a look at a similar question on SeqAnswers: How to use DESeq with non Integer values from mirdeep2