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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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How to merge two genes with overlapping positions but no overlapping CDS? #468

Open binzhengbin opened 1 week ago

binzhengbin commented 1 week ago

I tried to merge genes with overlapping regions using agat_sp_fix_overlaping_genes.pl but it failed because their CDSs don't overlap, is there any way to fix this? Thanks!

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Juke34 commented 1 week ago

This script if for a particular purpose and avoid overlap of the end of genes to be exactly at the same position ( a peculiarity for submission to public archive) You should use either the merge or complement script

binzhengbin commented 1 week ago

I don't quite understand what you mean, can you point me in the right direction? Or do you know of any code that accomplishes this?

Juke34 commented 1 week ago

If you work on 2 files use agat_sp_merge_annotations.pl

If you work on a single file then use the gxf2gxf script but you must first activate the merge option in the agat config file ( agat config —expose)

binzhengbin commented 1 week ago

I'll try your offer and I'll let you know if I hear anything new, thanks!

binzhengbin commented 1 week ago

Following your advice, I used agat_convert_sp_gxf2gxf.pl to merge overlapping genes, and it seemed to do something, but only the genes with overlapping CDS positions were merged, while the genes with overlapping other genes/mRNAs were not merged. 24A5B0557481EB48A8BB22CB2435E6F8

Juke34 commented 1 week ago

What vesion of AGAT do you use? To be able to merge gene without CDS, both gene must be of the same type (level1 must be similar e.g. gene and level2 must be of the same type e.g. mRNA). I keep in mind that they have to be on the same strand.

Juke34 commented 1 week ago

Right if two genes have CDS it is at CDS level that the overlap will be taken into account to decide to merge the gene or not. You would like to merge if it overlap at any level? This is something not implemented but if. houseful I could add it.

binzhengbin commented 1 week ago

Sorry, just saw the message now. It would be best if a gene level merge could be implemented.

binzhengbin commented 1 week ago

Since your agat_sp_fix_overlaping_genes.pl program only merges for CDS that have overlap, it would be a great creation if we could be allowed to autonomously choose the level of merging (e.g., gene, mRNA, exon, and CDS, etc.).