small rna analyse

[entomology]

I want to find micro rna from a non-model insect, no genome available, the only information I have now is the transcriptome (sra data from ncbi).

so

1 is it possible to predict micro rna from transcriptome of a species? is there any suitble pipeline of software available for it?

2 if the 1 method is not possible, I need to sequencing small rna from this species, after getting the data, what kind of software or is there stable pipeline for the analyze of the sequenced data?

I'm a newbian in NGS, hope to get help here, thank you in advance.

[entomology]

can anyone helpsome?

[lukas1848]

To answer your first question, you'd first of all need to know how the library was prepared. Cause if they did a polyA selection, you won't find any microRNAs.

[entomology]

To answer your first question, you'd first of all need to know how the library was prepared. Cause if they did a polyA selection, you won't find any microRNAs.

unfortunately, they did so..... but why? every eukaryotic organism has polya, why can't have microrna in it? I'm relatively fresh in small rna, thanks a lot for your help.

[lukas1848]

Poly A selection is used to isolate mRNAs so non-coding RNA won't make it to your final library and furthermore, if I'm not mistaken, in many library preps, smaller RNAs tend to be lost in column-based purification steps.

[entomology]

Poly A selection is used to isolate mRNAs so non-coding RNA won't make it to your final library and furthermore, if I'm not mistaken, in many library preps, smaller RNAs tend to be lost in column-based purification steps.

Thank you for your information. most of the transcriptome I'm interested is poly A based. I can save time from it now. actually, I'm doing small rna seq at the same time, and seems this is the best way to deal with it, hehe.