NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq
Kan Liu, Shangang Jia, Qian Du, and Chi Zhang
After the next-generation sequencing technology,
long-read sequencing technologies were developed. Both the
advantages and the drawbacks of long-read sequencing
technologies are obvious. Here, we take advantages of long-read
sequencing technology, MinION, to develop a comprehensive and
user-friendly pipeline, NanoAsPipe, to identify the transcriptomic
profiles, isoform profiles, and alternative splicing (AS) events of
long-read RNA-seq data. NanoAsPipe includes RNA-seq data
preprocessing, mapping and alternative splicing analysis to
simultaneously account for AS events. NanoAsPipe was applied
to two long-read datasets and its performance was evaluated by
comparing discovered AS events with gene annotation and
results from short-read RNA-seq data. Majority of predicted AS
events by NanoAsPipe was confirmed by the gene annotation and
there is a high correlation between results from long-read data
and short-read data.
This file contains the source code of NanoAsPipe and intructions for users.
This file contains test data sets for NanoAsPipe.