How to find overlapping coordinates of a gtf file

Question

[Apex92]

I am trying to list the entries of a gtf file (gencode.vM25.annotation.gtf) if they have overlap. I have been looking around for some tool to perform it - is there such a tool to do what I want? Thanks

[husensofteng]

You need to start with BedTools suite. It has many features to deal with coordinates, e.g cluster, merge, etc and the documentation is really easy to follow.

[Apex92]

This is definitely helpful - thank you

[Michael]

There are some tools to do interval overlap, bedtools and R/Bioconductor (rtracklayer+GenomicRanges) comes to mind. If you want to do it on the commandline use the former, or inside R use Bioconductor.

Answer 1

[lieven.sterck]

I assume you mean features in a GFF file that overlap other features in that same GFF file?

If so, have a look at AGAT , it certainly has some sub-programs that can do this.

here is more info: AGAT - Another Gff/Gtf Analysis Toolkit

[Apex92]

Yes, exactly I want to find the overlap between features in a GFF file with other features in that same GFF file. Thank you for your input.

Answer 2

[Alex Reynolds]

You could use BEDOPS gtf2bed and bedmap to map entries to themselves, filtering out any that are disjoint with awk and cut:

$ gtf2bed < annotations.gtf \
    | bedmap --count --echo --echo-map - \
    | awk -v FS="\t" -v OFS="\t" '($1 > 1)'  \
    | cut -f2- \
    > answer.bed

References:

• https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html
• https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html