making the most of rna-seq: pre-processing sequencing data with opossum for reliable snp variant detection [version 1; referees: 2 approved, 1 approved with reservations]

Clicks: 64
ID: 216853
2017
Free PDF
Article Quality & Performance Metrics
Overall Quality
Not rated
Combines reader engagement with the AI quality analysis. This article has not been analysed, so there is no overall score — reader engagement is measured and shown alongside.
AI Quality Assessment
Not analyzed
Readership in this journal
Emerging

Ranked #21 of 21 articles by views in ethnicity and disease

Most read Least read

Bar heights use a square-root scale.

Mint this article as an NFT
Not yet minted

Create a permanent, verifiable on-chain record of this article on the Scimatic Network. The NFT is held in your Journament account, and you can withdraw it to your own wallet at any time.

5 SUSD one-off · no wallet required
Sign in to mint
Abstract
Identifying variants from RNA-seq (transcriptome sequencing) data is a cost-effective and versatile alternative to whole-genome sequencing. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller. In this work, we show that using Opossum in conjunction with either Platypus or GATK HaplotypeCaller maintains precision and improves the sensitivity for SNP detection compared to the GATK Best Practices pipeline. In addition, using it in combination with Platypus offers a substantial reduction in run times compared to the GATK pipeline so it is ideal when there are only limited time or computational resources available.
Reference Key
oikkonen2017wellcomemaking Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Laura Oikkonen;Stefano Lise
Journal ethnicity and disease
Year 2017
DOI
10.12688/wellcomeopenres.10501.1
URL
https://wellcomeopenresearch.org/articles/2-6/v1
Keywords
bioinformaticsmedicinescience

Citations

No citations found. To add a citation, contact the admin at info@scimatic.org

Comments

No comments yet. Be the first to comment on this article.