Pipeline scripts for creating a miRspring (miRNA sequence profiling) document.
The product of this pipeline creates a miRspring document, which essentiallyis a small HTML javascript file. Each miRspring document has been developed in such a way that it reproduces miRNA sequencing data from a BAM file. Additionally it provides unique analysis tools, and does not need internet connectivity for these processes.
To create a miRspring document the scripts requires:
- a sorted BAM file and its index,
- Samtools.
- the following miRbase files: hairpin.txt, <species>.gff, mature.fa
- Perl
To test your system this repository contains small RNA data set (~100,000 reads) for which shell scripts have been prepared. Running these shell scripts will create a miRspring document if your system parameters have been set correctly.
Please visit the miRspring homepage for detailed information about the project.
