Analyzing high-throughput sequencing data for profiling microRNA expression
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FAQ

1. Installation in Ubuntu:
Please execute the following command in console terminal for installing the missing packages.

sudo apt-get install g++ libglib2.0-dev

Then, system will request your password and confirmation for installation.
After the installation, you can install miRExpress with no problem.

2. Installation in CentOS:
You need to have the privilege of administrator.
Please execute the following command in console terminal for installing the missing packages.

yum install gcc-c++ glib2-devel

After the installation, you can install miRExpress with no problem.

3. How to run mirExpress:
We strongly recommend you runing the "sh ExampleTest.sh" in folder "mirExpress/Example". 
If it worked successfully, you can modify this folder to run your own data.

4. Quickly checking my sequencing data is suitable for miRNA expression: 

After trimming 3' adaptor sequence, you could use the command "statistics_reads" to obtain the distribution of 
your sequencing data. There are three columns in the output file. The first column is read length. 
The second column is the number of unique reads. The third is the counts of reads.
Then, you could use this results to draw the read distribution. If the reads are abundant in 19~24 nt.
It it good for miRNA analysis. The example distribution could be downloaded.
This read distribution was produced by public domain data. 

5. How miRExpress profile miRNA expression:
miRExpress profiles miRNA expression according to the location of mature miRNA in the precursor
plus user defined tolerance range. 

About the command "analysis", the parameter of "-g" means the shifting range according to miRNAs.
For example, the position of hsa-let-7a in the precursor (hsa-let-7a-1) is 6~27. The default value of "-g" is 4. 
Therefore, the small RNAs which locate in 2~31 will be considerd as the expression of hsa-let-7a.
The expression of has-let-7a is computed by summing the sequence counts in that region.
You could also download the slide. 
It will help you to quickly understand how miRExpress profiles miRNA expression.