Question: Nanopore data to gtf/gff file
0
gravatar for I0110
9 months ago by
I0110120
United States
I0110120 wrote:

Hi,

I want to use Nanopore PCR-cDNA sequencing to detect known and novel isoforms in Arabidopsis under certain growth conditions. I am thinking to use minimap2 for mapping, alignment and error correction. If I want to get a gtf or gff from the mapped long reads, which software should I use? Or does minimap2 output a gtf/gff file?

Thanks!!!

sequencing assembly • 393 views
ADD COMMENTlink modified 9 months ago by colindaven2.1k • written 9 months ago by I0110120
1

Why not use stringTie? Note that minimap2 doesn't output a GTF.

ADD REPLYlink written 9 months ago by Devon Ryan94k

Just not sure if the long reads will not be assembled properly since I only used stringTie for illumina reads before. But I will try that first. Thanks!

ADD REPLYlink written 9 months ago by I0110120

StringTie2 is just released and appears to be a good solution for this problem: https://www.biorxiv.org/content/10.1101/694554v1

ADD REPLYlink written 8 months ago by I0110120
0
gravatar for colindaven
9 months ago by
colindaven2.1k
Hannover Medical School
colindaven2.1k wrote:

Long shot here, but you might get a first approximation using gmap with a GFF3 output mode.

It's very good, but if you are looking at error rich uncorrected reads it will mess up the ORFs due to sequencing artifacts.

That would be my choice, otherwise you can try to convert bam etc to GFF3 (perhaps via BED etc?).

ADD COMMENTlink written 9 months ago by colindaven2.1k

Can we use minimap2 to correct the error first and use the bam file output (I believe they should give a bam output) for GMAP GFF3 output mode? But then why we don't just do the minimap2 > stringtie as Devon suggested? Is there an advantage to use GMAP GFF3 output mode? Thanks!

ADD REPLYlink written 9 months ago by I0110120
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