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README
mirnaTA (miRNA Temporal Analyzer)
version 1.2.3
September 2014
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A. ABOUT
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The mirnaTA package (current version 1.2.3, released September 2014) can be downloaded from http://sourceforge.net/projects/mirnata/.
Language: PERL and R
Dependency: R statistical package (>= 2.13.0) http://cran.us.r-project.org/
After saving the mirnaTA_v1.2.3.tar into your directory, unpack the package as follows:
>tar -xvf mirnaTA_v1.2.3.tar
B. INPUT FILE REQUIREMENTS
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Input file must be tab-delimited and must contain at least 3 columns: the first column is the miRNA name, followed by a minimum of data from 2 time points.
Several example datasets are provided in the package under "example_datasets" directory.
Example 1: 3 time point data with no replicate where tp1=time point 1, tp2= time point 2, etc.
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mirna tp1 tp2 tp3
hsa-let-7a-5p 4 0 6
hsa-let-7a-3p 75 74 222
hsa-let-7a-2-3p 118 127 555
hsa-let-7b-5p 39 38 98
hsa-let-7b-3p 18 20 76
hsa-let-7c-5p 0 0 1
hsa-let-7c-3p 3 3 4
Example 2: 3 time point data with 2 replicates where rep1=replicate 1, rep2=replicate 2
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Note: The first column is miRNA name, followed by 3 columns of Replicate 1 data from three different time points, and then followed by another 3 columns of Replicate 2 data
mirna t1rep1 t2rep1 t3rep1 t1rep2 t2rep2 t3rep2
hsa-miR-8080 1886 1274 5024 5658 3822 15072
hsa-miR-8081 36 19 223 108 57 669
hsa-miR-8082 232 167 223 696 501 669
hsa-miR-8083 23 20 77 69 60 231
hsa-miR-8084 206 256 410 618 768 1230
hsa-miR-8085 24 6 42 72 18 126
hsa-miR-8086 113 121 86 339 363 258
hsa-miR-8087 0 0 13 0 0 39
hsa-miR-8088 15 13 22 45 39 66
hsa-miR-8089 0 7 0 0 21 0
C. HOW TO RUN mirnaTA:
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To learn how to run mirnaTA, type "perl nmrc_mirnata.pl --help".
Usage: nmrc_mirnata.pl --in <filename> --numrep 2 --tp 3 [options]>
parameters:
--in or -i Input data set
--numrep or -n Number of replicates
--tp or -t Number of time points
options:
--cor or -c Correlation coefficient (default=0.7)
--help Print this message
--version Print version information
Briefly, the syntax to run mirnaTA is as follows:
>perl nmrc_mirnata.pl -i <input_file> -n <x> -t <y>
where nmrc_mirnata.pl is the wrapper Perl script,
<input_file> is input file formatted as described above,
x = the number of replicates,
y = the number of time points.
(1) Example with 2 time points
>perl ./nmrc_mirnata.pl -i example_datasets/2tp1rep_dataset.txt -n 1 -t 2
OR
>perl ./nmrc_mirnata.pl --in example_datasets/2tp1rep_dataset.txt --numrep 1 --tp 2
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* Note: Make sure to create a new directory to save results from 'output_files" before running mirnaTA with new dataset since this would overwrite files.
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(2) Example with 3 time points and 1 replicate data
>perl ./nmrc_mirnata.pl -i example_datasets/human_3tp1rep_dataset.txt -t 3 -n 1
***(Note: here -t is 3 since there are 3 time points)
OR
>perl ./nmrc_mirnata.pl --in example_datasets/human_3tp1rep_dataset.txt --numrep 1 --tp 3
(3) Example with 3 time points and 2 replicates
>perl ./nmrc_mirnata.pl -i example_datasets/3tp2rep_dataset.txt -t 3 -n 2
***(Note: here -n is 2 since there are 2 replicates)
(4) Example with 3 time points and 3 replicates
>perl ./nmrc_mirnata.pl -i example_datasets/human_3tp3rep_dataset.txt -t 3 -n 3
***(Note: here -n is 3 since there are 3 replicates)
(5) Example with 5 time points
>perl ./nmrc_mirnata.pl -i example_datasets/5tp1rep_dataset.txt -t 5 -n 1
***(Note: here -t is 5 since there are 3 timepoints)
(4) Example with specific correlation coefficient, c
>perl ./nmrc_mirnata.pl -i example_datasets/5tp2rep_dataset.txt -t 5 -n 2 -c 0.9
***(Note: here -c is 0.9. The default value is 0.7)
E. VISUALIZATION:
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The mirnaTA generates a directory called 'output_files' containing several output files including a HTML file 'mirnata.html' file that you can view easily in a web browser. The mirnata.html contains:
(i) a histogram demonstrating the difference between raw data (prior to normalization) and quantile transformed data (post normalization),
(ii) a heatmap of differentially expressed miRNA species (P<0.05) identified using linear regression model
(iii) a heatmap of differentially expressed miRNA species (P<0.05) identified using non-linear analysis (CDF or ANOVA).
(iv) other intermediate files including quantile transformed data files, a list of significant miRNA species with their P-, slope, and intercept values
F. TROUBLESHOOTING:
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mirnaTA is a simple program and should run without any error provided that the input files are in the correct format. It is highly recommended that users try the package using either one or both sets of example data. After the example files produce the correct results, users are encouraged to try with their own data. In the case that it gives an error or crash without finishing, there are a few potential causes.
1. Potential problem: R package is not installed.
Solution: If you are getting error message such as 'Can't exec Rscript', you probably do not have R package installed. R package can be downloaded from (http://cran.us.r-project.org/).
2. Potential problem: No heat map is generated.
Solution: mirnaTA requires gplots and although the mirnaTA contains script to install this library, it may be that you need to install it manually.
3. Potential problem: You input files are not in the correct format.
Solution: Check the example datasets and make sure that your files follow the same format. There must be at least two time points in tab-delimited format.
G. DISCLAIMER:
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Copyright 2013-2014
microRNA Temporal Analyzer (mirnaTA version 1.2.2)
Genomics and Bioinformatics Department
Biological Defense Research Directorate (BDRD)
Naval Medical Research Center-Frederick (NMRC-Frederick), Fort Detrick, Maryland
mirnaTA is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. mirnaTA (version 1.2.0) is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
H. CONTACT INFO:
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Contact: Please send questions and comments to regina.cer@med.navy.mil or cer.regina@gmail.com.
Thank you for your feedback.
Download Latest Version
mirnaTA_v1.2.3.tar.gz (8.1 MB)
