Nov 14, 2013

On the optimal trimming of high-throughput mRNA sequence data

BioRxiv : the Preprint Server for Biology
Matthew D MacManes

Abstract

The widespread and rapid adoption of high-throughput sequencing technologies has changed the face of modern studies of evolutionary genetics. Indeed, newer sequencing technologies, like Illumina sequencing, have afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Computer Software
Study
Genome
Research Personnel
Nucleic Acid Sequencing
Sequencing
Adaptation
High Throughput Analysis
Nucleotides
Molecular Genetic Technique

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.