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sRNAflow – a tool for analysis of small RNA-seq data



Funding: European Regional Development Fund (ERDF) “On Implementation of Activity “Post-doctoral Research Aid” of the Specific Aid Objective 1.1.1 “To increase the research and innovative capacity of scientific institutions of Latvia and the ability to attract external financing, investing in human resources and infrastructure” of the Operational Programme “Growth and Employment”

Project Title: sRNAflow – a tool for analysis of small RNA-seq data

Project Nr.:

Period: 36 month (1st September 2017 – 31 st August 2020)

Project costs: 133 806,00 EUR

Project implementer: Dr.biol. P. Zajakins

 The goal of this project is to develop sRNAflow - a software tool for analysis of small RNAs, which would not require advanced computer skills from the user. The tool will include some specific novel algorithms necessary for analysis of samples obtained from biofluids. Many already existing tools for adapter removing, quality check, mapping reads, counting, differential expression analysis, non-template isomiRs search, and for the miRNA target prediction will be integrated into software. This tool will produce united report for all steps of workflow. This project is focused on needs of the inexperienced user to keep this tool simple to use.

Information published: 01.09.2017.


Progress of the project

1 September 2017 - 30 November 2017

During these three months, using the R programming language and publicly available software packages, the "alpha" version of the software program has been developed. It is includes, at the moment, a quality check with fastqc before and after the removal of the adapters, a representative random subset of sample comparing against the NR database, using the blastn tool, mapping of the sample to the full human genome (Ensembl database), alignments repositioning, based on the local coverage with the ShortStack algorithm, creation of a catalog of expressed RNA types using Ensembl's human genome annotation and miRNA differential expression analysis using DESeq2.

The project was popularly presented to the wider community within the framework of "Scientists' Night" activities.

Information published: 30.11.2017.


Progress of the project

1 December 2017 - 28 February 2018

During these three months, a new version of the program has been developed. It's corrects various errors and have such additional functionality as a differential expression analysis using DESeq2 for all classifiable RNA types. It introduces the analysis of the overlap of the classified RNA types. Has been developed the prioritisation algorithm of building of catalog of expressed RNA types, which allows to solve the problem with an annotation overlap. Started work on the BLAST rating sorting algorithm.

Participated in the "3rd OpenMultiMed Training School. Multi-scale and Multi-level Modelling Methodologies in Biomedicine".

Information published: 28.02.2018.

Mājas lapas izstrādi finansēja ERAF aktivitātes projekts Nr. 2010/0196/2DP/ "Latvijas biomedicīnas pētījumu integrācija Eiropas zinātnes telpā".