Getting the overlap between two GTF files

Question

[feather-W]

Hello,

I have two GTF files which contain the information of transcripts, and I want to get the overlap of transcripts between the two GTF file. Can anyone give me some advice?

Thanks!

[feather-W]

Ok, thanks for all of your help very much! I will try it.

Answer 1

[rfran010]

Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly.

If it's not done already, you can filter for transcripts only of each file, then use bedtools:

awk '$3 == "transcript"' file1.gtf > file1.txOnly.gtf
awk '$3 == "transcript"' file2.gtf > file2.txOnly.gtf

bedtools intersect -u -a file1.txOnly.gtf -b file2.txOnly.gtf > file1_tx_overlapping_file2_tx.gtf

depending on your exact goals for what overlaps you want reported you can switch the -a and -b files or adjust options.

Answer 2

[Pierre Lindenbaum]

bedtools intersect \
    -a  <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf  | sort -t $'\t' -k1,1 -k2,2n ) \
    -b  <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file2.gtf  | sort -t $'\t' -k1,1 -k2,2n )

Answer 3

[GenoMax]

Something in AGAT should work: https://agat.readthedocs.io/en/latest/?badge=latest

[Alex Reynolds]

What would that be?

[Juke34]

The script agat_sp_compare_two_annotations.pl or agat_sp_sensitivity_specificity.pl
But if you are interested in the ranges then bedtools bedops or awk will be your friend

[Alex Reynolds]

It would be helpful if recommendations for toolkits included actual solutions.

[GenoMax]

Since I had not recommended a specific script in AGAT I had posted this as a comment so OP can check the documentation on their own. If Juke34 (author of AGAT) wants to post a stand-alone answer we can delete my original comment.

Answer 4

[Alex Reynolds]

Using bedops --intersect and gtf2bed will get their common genomic space:

bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2bed < transcripts.gtf) > answer.bed

If you want to know what transcripts overlap other transcripts, specifically, you could use bedmap --echo --echo-map:

bedmap --echo --echo-map <(gtf2bed < transcripts.gtf) > answer.bed

More information at: https://bedops.readthedocs.io/