The impact of read length on quantification of differentially expressed genes and splice junction detection.

ABSTRACT:

Background

The initial next-generation sequencing technologies produced reads of 25 or 36 bp, and only from a single-end of the library sequence. Currently, it is possible to reliably produce 300 bp paired-end sequences for RNA expression analysis. While read lengths have consistently increased, people have assumed that longer reads are more informative and that paired-end reads produce better results than single-end reads. We used paired-end 101 bp reads and trimmed them to simulate different read lengths, and also separated the pairs to produce single-end reads. For each read length and paired status, we evaluated differential expression levels between two standard samples and compared the results to those obtained by qPCR.

Results

We found that, with the exception of 25 b

SUBMITTER: Chhangawala S 

PROVIDER: S-EPMC4531809 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature