Hi, agat_sp_gxf_to_gff3.pl do the trick! However, is it a possible to see all entries it have been updated? For example, it output in console:
Primary tag values (3rd column) not expected => region inverted_repeat sequence_feature cdna_match repeat_region -
- Those primary tag are not yet taken into account by the parser! -
- If you wish to use it/them, pleast update the parameter feature json files accordingly (features_level1, features_level2 or features_level3). -
- To resume: -
- * it must be a level1 feature if it has no parent. -
- * it must be a level2 feature if it has a parent and this parent is from level1. -
- * it must be a level3 feature if it has a parent and this parent has also a parent. -
- -
- Currently the tool just ignore them, So if they where Level1,level2, a gene or RNA feature will be created accordingly.
How I could see how is that incorrect tags? And entries?
Primary tag values (3rd column) not expected => lnc_rna -
- In theory these values are not compatible with gff3 format because they are not part of the Sequence Ontology. -
- If you want to follow rigourously the gff3 format, please visit this website: -
- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md -
- They provide tools to check the gff3 format. -
- Even if you have this warning, you should be able to use the gff3 output in most of gff3 tools.
Same here.
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* Check1: _check_sequential *
**********************************
We found 2 cases where part of the locus data where defined earlier in the file.
done in 0 seconds
How I could see how is these cases? And entries? To correct it. There are an output resume file?
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* Check2: _check_l2_linked_to_l3 *
**********************************
We fixed 3160 cases where L2 and L1 features were missing
done in 351 seconds
same here.
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* Check4: _remove_orphan_l1 *
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We removed 10 level1 features that had no subfeature linked to it.
done in 0 seconds
Same here.
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* Check5: _check_exons *
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_check_exons We modified the L2 RIGHT extremity !
_check_exons We modified the L2 RIGHT extremity !
We create 73 exons that were missing
We modified 7 exons positions that were wrong
done in 19 seconds
Here too.
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* Check7: _check_all_level2_posi *
* tions *
**********************************
We fixed 3 wrong level2 position cases
done in 13 seconds
Here too.
**********************************
* Check8: _check_all_level1_posi *
* tions *
**********************************
We fixed 5 wrong level1 position cases
done in 1 seconds
Too.
Thank you!
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marcelolaia •
It is certainly worth a try. The
-t exonoption specifies the GTF feature type in column 3 of the GTF/GFF3 that featureCounts uses. I suggest you do a small experiment by changing the CDS term in the third column to exon for a couple of genes and see whether it works. Please do post your findings here for the benefit of the community.