Mir-RNA analysis by RNA-seq data

Question

[lkianmehr]

Hello to all!

I am gonna identify mir-RNA from RNA-seq reads, but it's the first time I am working for mir-RNA. is it same with RNA-seq workflow just replace GTF with gff3 (from mir-Base)? if yes what is the application of hairpin and mature in this regard? I would be appreciated if somebody can explain me at first step?

thanks in advance

[ATpoint]

Is this now a wet-lab or a computational question? The point with miRs is that they are (obviously) small. Typically standard RNA-seq protocols use a certain fragment size after shearing the cDNA for sequencing, which is larger than the processed miRs. Please elaborate on what exactly the question is.

[lkianmehr]

sorry, I edited my question, I mean just is bioinformatic workflow. I have a series of RNA-seq data and I am gonna to find known Micro-RNAs on them. I didn't know any about details of alignment and finally the differential expression analysis of micro-RNA if maybe please explain about that.

[WouterDeCoster]

As ATpoint already mentioned "standard" RNA-seq protocols select against short RNA species such as miRNAs.

[WouterDeCoster]

This question is quite unclear. One sentence is about library prep, the second is suddenly about GTFs and GFF3s. It is unclear which data you have currently.

If you have question about library prep then SEQanswers would be more appropriate.

[lkianmehr]

I have edited the question, I just want to know about the bioinformatic workflow details of micro-RNA analysis by RNA-seq data.

[seta]

Hi lkianmehr, I have the same issue, please let me know if you find any solution?

thanks