pipeline for the analysis of small RNA data
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README.md

Repo related to this paper (Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis) is here: https://github.com/lpantano/small-RNA-analysis

seqbuster

Please, be aware that the user firendly interface is depecrated. SeqBsuter only keeps updated miraligner as an independet file. Read how to annotate miRNAs/isomiRs from fastq files here: http://seqcluster.readthedocs.org/mirna_annotation.html

Some comparison between many tools here.


Project Status: Inactive - The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.

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Cite

SeqBuster is a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Pantano L, Estivill X, Martí E. Nucleic Acids Res. 2010 Mar;38(5):e34. Epub 2009 Dec 11.

Seqbuster as published in 2010

Note:All the below doc is updated and only are here for historical reason

See our documentation page

small RNA analysis of deep sequencing data. SeqBuster offers four tools to analyze all your small RNA data coming from Illumina sequencing.

  • Installation
  • adapter removal: remove 3' adapter
  • miraligner: miRNA annotation using miRBase database
  • R package isomiRs to visualize isomiRs and miRNA abundances in a group of samples (new)
  • seqcluster analyzes the rest of small RNAs and annotate to multiple databases in bed format (new)
  • SeqBuster team updates periodically the tools with more information about how to be used and new applications. If you have any comment please use: mailing-list. Also visit our blog or facebook or twitter to be up-to-day of the new information added in the wiki.

The development of Seqbuster was partly funded by the EU Seventh Framework Programme [FP7/2007-2013, grant number 262055, ESGI]. http://www.esgi-infrastructure.eu/#