small RNA-Seq

[aquleaf]

Hi.

We have small RNA-Seq data. We try to find out microRNAs. Could anyone recommend a software or pipeline to analyse the small RNA data?

Wish your help! Thanks very much!


Best, Mei

[mnkyboy]

There are some nice commercial tools like CLC and GeneSifter we use that we are happy with but I have also been fairly happy with mirdeep2 as an open source option once you get some of the kinks for input worked out. I routinely use this for fast QC and adapter removal.

[xyzwujun]

Hi.

We have small RNA-Seq data. We try to find out microRNAs. Could anyone recommend a software or pipeline to analyse the small RNA data?

Wish your help! Thanks very much!


Best, Mei

Hi , I am not sure about detailed information in your experiment, for example, species or genome sequencing available. miDeep indeed can identify the mature microRNA, but more powerful for mammal species. If your experiment just involved microRNA frequently profiling species like human or mouse etc, you can use alignment tool ( like bowtie ) against anntotated miRNAs from miRbase.

Thanks,

[aquleaf]

Thanks very much!

Are there any other tools to discover novel microRNAs from small RNA-Seq?

Our experiments were taken in Drosophila melanogaster by illumina.

[xyzwujun]

Maybe try miRanalyzer pipline.