Question: Tools For De Novo Assembly Of Mirnas?
2
gravatar for Ahdf-Lell-Kocks
7.1 years ago by
Ahdf-Lell-Kocks1.6k
Ahdf-Lell-Kocks1.6k wrote:

Are there any tools that will do de novo assembly of miRNAs from next-gen sequencing data of reads of 36bp or shorter for which there is no reference genome?

ADD COMMENTlink modified 7.1 years ago by Rm7.8k • written 7.1 years ago by Ahdf-Lell-Kocks1.6k
1

For what I know, a friend of mine is developing a method to do such thing. He is in MDC, Berlin. They use reads to assemble contigs and use a naive Bayesian method to classify the result. But they haven't finish it yet.

Genome Reference freE Prediction of miRNA : mirGREP

It is the name of the method.

ADD REPLYlink written 7.1 years ago by Ning-Yi Shao380

... for which there is no reference genome.

ADD REPLYlink written 7.1 years ago by 2184687-1231-83-4.9k
3
gravatar for Rm
7.0 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

mature miRNAs are around 22bases (range: 16 to 32): I think there is no need to assemble. Reads potentially represents complete mature miRNA's, if small RNA extraction protocols are followed before sequencing.

If you don't have reference genome. Best way to get potential microRNAs is to map the reads to the complete miRbase ; say using miRNAKEY; And also map using mirdeep2 or other tools to the nearest homologous genome whose sequence is available. Then blast or blat the potentials reads obtained to the NT or EST databases to see if any potentials hits in the genome of your interest.

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Rm7.8k

Thanks, very useful comments. I did try Trinity's clustering step, and it does find a bunch of clusters of 10-15 36bp reads with an offset of 1bp, but according to what you say, these shouldn't be mature miRNAs, right?

ADD REPLYlink written 7.0 years ago by Ahdf-Lell-Kocks1.6k
2
gravatar for Nicolas Rosewick
7.1 years ago by
Belgium, Brussels
Nicolas Rosewick7.5k wrote:

de novo assumes you don't have a reference genome. Is that true ?

If you have a reference genome, try mirDeep

ADD COMMENTlink written 7.1 years ago by Nicolas Rosewick7.5k

Yes, for which there is no reference genome.

ADD REPLYlink written 7.1 years ago by Ahdf-Lell-Kocks1.6k
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