# Welcome to seqbuster/seqcluster’s documentation!

Analysis of small RNA sequencing data. It detect unit of transcription over the genome, annotate them and create an HTML interactive report that helps to explore the data quickly.

Contents:

- Installation
  - Seqcluster
  - Tools dependecies for a full small RNA pipeline
  - Data
  - R package
- Citation
- Getting started
  - clustering of small RNA sequences
  - Interactive HTML Report
  - Easy start with bcbio-nextgen.py
- Outputs
  - seqcluster
  - Report
- Examples of small RNA analysis
  - miRQC data
- miRNA annotation
  - Processing of reads
  - Prepare databases
  - miRNA/isomiR annotation with JAVA
  - Convert to GFF3-srna
  - Post-analysis with R
  - Manual of miraligner(JAVA)
- Collapse fastq(.gz) files
- Handling multi-mapped reads
- Tools for downstream analysis
  - Web-servers
  - Command-lines
- Relevant papers about isomiRs and other novel small RNAs with functional relevance
  - Validation
  - IsomiRs
  - General
  - Targets
  - Techonolgy
- Documentation
- Classes

Visit GitHub code

I am in the process to document all classes and methods

# Indices and tables

- Index

- Module Index

- Search Page