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mirdeep2 step-by-step tutorial

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!

rna-seq sequencing next-gen
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updated by Biostar Biostar • written by robm9119 robm9119

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

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written by igor igor

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

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written by realnewbie • realnewbie

2 answers

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

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written by gzl • gzl

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

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written by Ram Ram

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/

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written by gzl • gzl

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

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written by Mike Lafferty • Mike Lafferty

The link is broken !

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written by Björn • Björn

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/

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written by gzl • gzl

Please use ADD COMMENT/ADD REPLY to reply to an earlier answer, as such threads remain logically structured and easy to follow.

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written by WouterDeCoster WouterDeCoster

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