Finding the maximum intron length from aligned exomic data

Question

[GLFrey]

Hello,

I'm currently working on some plant exomic data and I need to calculate the maximum intron length, I've done some searching and found answers for RNA-Seq but not exome seq and I was wondering if anyone could help me with some suggestions regarding any methods or point me towards any literature calculating maximum intron length in exomic data? The annotations for the reference genome for the species I am working with does not contain any information on introns at all.

Thank you.

[Ram]

maximumintronlength makes no sense as a tag. Maybe add better, more relevant tags?

Answer 1

[h.mon]

edit: I pointed to a fork of the old GFFutils. The repository for this old version is https://github.com/daler/GFFutils_old, and the repository for the current version is https://github.com/daler/gffutils.

end of edit.

What is the genome you are working with? What is the format of the annotation? If the annotation contains information on exons, it does contain on introns as well: introns are delimited by same-gene exons boundaries.

Some pointers for GTF / GFF files:

https://github.com/seandavi/GFFutils (see the Imputing introns section)

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Intron size from gtf/gff file ?

http://bioops.info/2012/11/intron-size-gff3-perl/

And this gist with a perl script.

[GLFrey]

Hello h.mon,

Once again, thank you for your help. The genome annotation is for wheat and the annotation files are in GTF and GFF3 format. I will have a look through the links you have posted.

Thank you!

[h.mon]

In particular, have a look at the GFFutils repository, there is a section titled Imputing introns

[GLFrey]

Thank you so much for this, h.mon it looks perfect.