mirdeep2 step-by-step tutorial

Question

[robm9119]

Hi folks,

Does anyone know of any tutorial for running mirdeep2? I tried mirdeep2's own manual:

https://www.mdc-berlin.de/36105849/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/documentation

but couldn't make sense of the directions. If anyone knows of a good tutorial with details of running the tool and kindly share it, I will be really grateful!

[igor]

It looks like it's just one step. Which part specifically did you have a problem with?

[realnewbie]

Hi, In case someone still needs it, here is the tutorial I found s/he can try (adapted from mirdeep2 tutorial) in this website.

Answer 1

[gzl]

Here, is an easy to follow tutorial of miRDeep2. http://petang.cgu.edu.tw/Bioinfomatics/Lecture/0_HTS/04/20120316.pdf

[Ram]

This tutorial is incomplete without the "preliminary" files it uses. Maybe host them on the cloud and add them to the tutorial if possible?

[gzl]

Sorry, I do not have this data. However, You can download any miRNA-seq data from NCBI-GEO or SRA. For instance you can start with C.elegan miRNA-seq from a Geo data set with an identifier GSE60419. Use SRAtoolkit to download the raw data and afterwards you can proceed with the miRDeep2 pipeline.

The whole genome of C.elegen can be downloaded from here. http://support.illumina.com/sequencing/sequencing_software/igenome.html

whereas mature and precursor miRNAs can be downloaded from miRBase current release. ftp://mirbase.org/pub/mirbase/CURRENT/

[Mike Lafferty]

This link is now broken. Do you know if the file is still accessible elsewhere?

[Björn]

The link is broken !

[13530213]

http://petang.cgu.edu.tw/Bioinfomatics/Lecture/0_HTS/2015/04/