Impact of sequencing depth and technology on de novo RNA-Seq assembly.

ABSTRACT:

Background

RNA-Seq data is inherently nonuniform for different transcripts because of differences in gene expression. This makes it challenging to decide how much data should be generated from each sample. How much should one spend to recover the less expressed transcripts? The sequencing technology used is another consideration, as there are inevitably always biases against certain sequences. To investigate these effects, we first looked at high-depth libraries from a set of well-annotated organisms to ascertain the impact of sequencing depth on de novo assembly. We then looked at libraries sequenced from the Universal Human Reference RNA (UHRR) to compare the performance of Illumina HiSeq and MGI DNBseq™ technologies.

Results

On the issue of sequencing depth, the amount of

SUBMITTER: Patterson J 

PROVIDER: S-EPMC6651908 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature