How to identify mRNAs, transcription start/stop sites and regulatory elements from MinION data

Question

[Kumar]

I am looking to analyze minION data for identifying  mRNAs, transcription start/stop sites and regulatory elements. I am using minimap2 and graphmap for alignment and got .sam files. I am not sure how to process these files to identify transcription start/stop sites, regulatory elements and mRNAs.

I am following several commands of graphmap to generating .sam files. For instance,

./graphmap owler -r reads.fa -d reads.fa -o overlaps.mhap
./graphmap align -r scerevisiae.fa --gtf scerevisiae.gtf -d reads.fastq -o alignments.sam ./graphmap align -r escherichia_coli.fa -d reads.fastq -o alignments.sam --extcigar

Do I need to use IGV for visualization? Else any other pipeline to identify regulatory elements.

[Asaf]

Visualization is always good and IGV is a great choice. Before starting I would make sure:

1. What is the starting material? Was it mRNA? DNA? poly-A selected RNA?
2. Mapping is valid i.e. nice coverage, reads are mapped with high quality etc.

[Kumar]

How I can get these questions? Do I need to use .bam file, generated from graphmap and see using IGV?

[WouterDeCoster]

Else any other pipeline to identify regulatory elements.

How do you envision finding regulatory elements? Per definition these are not transcribed, so you won't have data about them from transcriptome sequencing.