Comparisons of genes coordinates

Question

[nlehmann]

Hi,

I would like to compare genes coordinates between 2 GTF/GFF files. I tried using Gffcompare but the classification codes depends on the introns chains. I thought of something simpler, that would compare gene lengths and say if genes are equal, longer in 3' or longer in 5'. Let's take an example with longer in 3':

> cat A.gff3
chr1    ncbiRefSeq  gene    5000    8000    .   +   .   ID=gene1;Name=gene1
chr1    ncbiRefSeq  transcript  5000    8000    .   +   .   ID=XM_gene1;Parent=gene1
chr1    ncbiRefSeq  exon    5000    5524    .   +   .   Parent=XM_gene1
chr1    ncbiRefSeq  exon    6755    6829    .   +   .   Parent=XM_gene1
chr1    ncbiRefSeq  exon    7800    8000    .   +   .   Parent=XM_gene1

> cat B.gff3
chr1    ncbiRefSeq  gene    5000    10000   .   +   .   ID=gene1;Name=gene1
chr1    ncbiRefSeq  transcript  5000    10000   .   +   .   ID=XM_gene1;Parent=gene1
chr1    ncbiRefSeq  exon    5000    5524    .   +   .   Parent=XM_gene1
chr1    ncbiRefSeq  exon    6755    6829    .   +   .   Parent=XM_gene1
chr1    ncbiRefSeq  exon    7800    10000   .   +   .   Parent=XM_gene1

The comparison of these two GFF3 files should show that gene1 in B.gff3 is longer in 3' than A.gff3. I thought also of using bedtools overlap but this wouldn't give enough details (would just return that the genes overlap but we don't know how). If the gene in B started upstream (e.g. 4000), we should get the information that this gene is longer in 5' and in 3' in B compared to A.

Using gffcompare, the 2 genes are considered as equal because they have the same intron chains:

 > gffcompare -r A.gff3 B.gff3
 > cat gffcmp.B.gff3.tmap
ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM  TPM cov len major_iso_id   ref_match_len
gene1   XM_gene1    =   gene1   XM_gene1    3   0.000000    0.000000    0.000000    2801    XM_gene1    801

Thanks for the help.

[GenoMax]

Have you tried agat_sp_compare_two_annotations.pl from AGAT?

[nlehmann]

Yes, but it just gives genes that overlap between the 2 inputs, with no details on the way they overlap.