Question: Mir-RNA analysis by RNA-seq data
0
gravatar for lkianmehr
12 weeks ago by
lkianmehr10
France
lkianmehr10 wrote:

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

rna-seq mir-seq • 202 views
ADD COMMENTlink modified 10 weeks ago by Biostar ♦♦ 20 • written 12 weeks ago by lkianmehr10
1

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.

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by ATpoint7.5k

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.

ADD REPLYlink written 12 weeks ago by lkianmehr10

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

ADD REPLYlink written 12 weeks ago by WouterDeCoster32k

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.

ADD REPLYlink written 12 weeks ago by WouterDeCoster32k

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

ADD REPLYlink written 12 weeks ago by lkianmehr10
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