miRPIPE

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

miRPIPE program

Simple programs to parallelize the analysis of miRNA in human samples with sRNAtoolbox (https://bioinfo2.ugr.es/srnatoolbox/).

Feel free to parallelize your own projects.

Installation

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

Scripts

1. batch_prepro_bench.sh

1. Creating working directory with these folders:

• data for the downloaded samples
• logs for the log files that you can check if there is any error
• batch for the batch files in .bat format
• results for the results

2. Creating batch file for sRNAbench analysis.

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:

• /home/user/working_directory/experiment/batch/prepro.bat. An optionally batch file output. Running it you will download the samples parallely if you have not done before.
• /home/user/working_directory/experiment/batch/bench.bat. Runnng it you will perfom sRNAbench analysis.
• /home/user/working_directory/experiment/logs/parameter_file.txt. Samples report. It will be used by other scripts.

2. DE.sh

Creates a batch file that you can run to analyze the differential expression of your data.

USAGE:

sh DE.sh /home/user/working_directory /path/to/SraRunTable.txt column

In column, type the name of the SRA Table's column where it is the phenotypes conditions.

OUTPUT:

/home/user/working_directory/experiment/batch/DE.bat. Running it you will also run parallely both miRBase and miRGeneDB differential expression analysis.

3. quality_creator.sh

A simple script to parallelize quality sRNAbench analysis.

USAGE:

Usage: sh batch_QUALITY.sh QUALITY_parameter_file.txt

In parameter file, type 0 for mean analysis, 1 for min analysis or 2 for noMM=0. You have a QUALITY_parameter_file.txt example in the documentation.

OUTPUTS:

• /home/user/working_directory/experiment/batch/quality_analysis_commands.bat. Running it you will also run parallely BATCH QUALITY for all the analysis indicated before.
• /home/user/working_directory/experiment/batch/quality_boxplot_commands.bat. Running it you will also run parallely BATCH QUALITY BOXPLOT for all the analysis indicated before.

4. batch_QUALITY.sh

Creates a batch file for quality sRNAbench analysis parallely.

USAGE:

sh batch_QUALITY /home/user/working_directory /path/to/SraRunTable.bat mean_or_min_or_noMM Q

Type 0 for mean analysis, 1 for min analysis or 2 for noMM=0

OUTPUTS:

The output will be generated in the batch folder. Example: /working_dir/experiment/batch/batch_QUALITY_type_20SRP049635.bat. Running it you will run BATCH_QUALITY script parallely for all the analysis indicated in the parameter file.

5. input_ggplot_quality.sh

Create the input to generate a boxplot to visualize the quality in the isoMiRs profiles with ggplot package in R.

USAGE:

sh batch_ggplot_quality.sh /home/user/working_directory /path/to/SraRunTable.batt folder_output_name

OUTPUTS:

The output will be generated in the logs folder. Example: /working_dir/experiment/logs/folder_output/input_+.txt.

6. ggplot_quality.R

Visualization of the quality impact in isomiRs and other variants with ggplot package in R.

USAGE:

Rscript ggplot_quality.R results_directory path_to_input

OUTPUTS:

The output will be generated in the results_directory that you have to create previously.