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Simple scripts to parallelize miRNA analysis with sRNAtoolbox performed for my Master thesis.

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Name		Name	Last commit message	Last commit date
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miRPIPE		miRPIPE
LICENSE		LICENSE
README.md		README.md

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miRPIPE

This is my Master Thesis project at the University of Granada (UGR).

miRPIPE program

In this miRPIPE directory there are scripts that you can run to reanalyze the data. Also feel free to use with your own data.

Installation

Download the miRPIPE folder from https://github.com/marromesc/miRPIPE/tree/master/miRPIPE
Move it to your opt folder. mv miRPIPE.zip /home/usr/opt/miRPIPE.zip
Unzip unzip miRPIPE.zip
Run one by one for each script: chmod +x script_name.sh

Scripts

Scripts create a working directory and batch files that you have to run to start the analysis.

batch_prepro_bench.sh

Usage: batch_prepro_bench.sh /home/user/working_directory /path/to/SraRunTable.txt samples_downloaded adapter_ask adapter_sequence If you have already downloaded the samples type 1 in samples_downloaded. If not, type 0. If adapter_ask is 0, it means that there is no adapter. Type 1 in adapter_ask to guess the adapter or 2 if there is an adapter.

OUTPUTS: