Required features in GTF file.

hartleys / JunctionSeq

The JunctionSeq R package is a powerful tool for testing and visualizing differential usage of exons and splice junctions in next-generation, high-throughput RNA-Seq experiments.

28 stars 15 forks source link

Required features in GTF file. #21

Closed brgew closed 7 years ago

brgew commented 7 years ago

26 April 2017

Hi,

I wonder what feature types are required in the GTF file used by QoRTs, only 'exon's, as for DEXSeq, or are others required?

Thank you for these programs!

hartleys commented 7 years ago

The exon lines are the most important by far. There are a few things that are needed by one or two specific metrics, but that are not needed in order for QoRTs to run.

Specifically:

In order to generate the UTR vs coding metrics, you will also need the "CDS" lines.
In order to calculate the "biotype" metrics, you'll obviously need the biotype optional tags.

QoRTs ignores all lines other than "CDS" and "exon".