False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors.

ABSTRACT: Sequence similarity among distinct genomic regions can lead to errors in alignment of short reads from next-generation sequencing. While this is well known, the downstream consequences of misalignment have not been fully characterized.  We assessed the potential for incorrect alignment of RNA-sequencing reads to cause false positives in both gene expression quantitative trait locus (eQTL) and co-expression analyses. Trans-eQTLs identified from human RNA-sequencing studies appeared to be particularly affected by this phenomenon, even when only uniquely aligned reads are considered. Over 75% of trans-eQTLs using a standard pipeline occurred between regions of sequence similarity and therefore could be due to alignment errors. Further, associations due to mapping errors are likely to misleadi

SUBMITTER: Saha A 

PROVIDER: S-EPMC6305209 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature