Computing intron length per trancript

Question

[EVR]

Hi,

I have a GFF3 file and I would like to compute the intron length per transcript from GFF3 file. Any guidance would be highly appreciated. Thanks in advance.

[WouterDeCoster]

What have you tried?

[EVR]

I tried a tool called "Quast" but it gave only the minimum, maximum and average intron length of transcripts and overall summary of genome.

[WouterDeCoster]

I'm not aware of a tool that does what you need (but it might exists nonetheless). I guess you need to do some scripting, and essentially I would approach this as intron_length = transcript_length - (sum of exons and UTRs). As you can see the third field contains features such as 'exon', 'gene', 'transcript', and the last field contains information about the 'parent' transcript and gene a feature belongs to.