Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 54,982 bioRxiv papers from 253,713 authors.

Alignment and mapping methodology influence transcript abundance estimation

By Avi Srivastava, Laraib Malik, Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Michael I Love, Carleton Kingsford, Rob Patro

Posted 03 Jun 2019
bioRxiv DOI: 10.1101/657874

The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been shown to be important, considerably less attention has been given to comparing the effect of various read alignment approaches on quantification accuracy. We investigate the effect of mapping and alignment on the accuracy of transcript quantification in both simulated and experimental data, as well as the effect on subsequent differential gene expression analysis. We observe that, even when the quantification model itself is held fixed, the effect of choosing a different alignment methodology, or aligning reads using different parameters, on quantification estimates can sometimes be large, and can affect downstream analyses as well. These effects can go unnoticed when assessment is focused too heavily on simulated data, where the alignment task is often simpler than in experimentally-acquired samples. We discuss best practices regarding alignment for the purposes of quantification, and also introduce a new hybrid alignment methodology, called selective alignment (SA), to overcome the shortcomings of lightweight approaches without incurring the computational cost of traditional alignment.

Download data

  • Downloaded 842 times
  • Download rankings, all-time:
    • Site-wide: 7,695 out of 54,982
    • In bioinformatics: 1,382 out of 5,689
  • Year to date:
    • Site-wide: 983 out of 54,982
  • Since beginning of last month:
    • Site-wide: 38 out of 54,982

Altmetric data

Distribution of downloads per paper, site-wide

Sign up for the Rxivist weekly newsletter! (Click here for more details.)