Yes, we’ve seen this. Our gff3toolkit software can detect and fix these errors. https://github.com/nal-i5k/gff3toolkit
You first need to run gff3_QC. This creates an output file with all the errors in the gff3 file. To have it fix just the mismatched feature boundaries, you need to create a new error file with 1) the header from the error file and 2) all the lines with error code Ema0003 (see https://github.com/NAL-i5K/GFF3toolkit/blob/master/docs/Detection-of-GFF3-format-errors.rst for all the error codes). gff3_fix will update the coordinates of the parent by using the minimum and the maximum coordinate of the child feature.
e.g.
#detect errors
gff3_QC -g example_file/example.gff3 -f example_file/reference.fa -o error.txt -s statistic.txt
#create file to fix just Ema0003 errors (although you can have it fix more types of errors if you want)
head -1 error.txt > errors-for-gff3fix.txt
grep Ema0003 error.txt >> errors-for-gff3fix.txt
#run gff3 fix
gff3_fix -qc_r errors-for-gff3fix.txt -g example_file/example.gff3 -og corrected.gff3
#I like to run gff3_QC again on the output as a sanity check
gff3_QC -g corrected.gff3 -f example_file/reference.fa -o corrected-error.txt -s corrected-statistic.txt
Hth, let me know if you run into any snags.
Monica
Has anyone had issues with the GFF pulled from Apollo where sub-feature coordinates extend beyond parent features (e.g., exon extends beyond mRNA), even though the visualization of the features is correct? I have several instances where the sub-feature coordinates are correct, but the feature coordinates are not. Please see attached picture as an example, coordinates are highlighted.Each issue has been with a user-created/edited track. Thanks!
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Le 19 sept. 2024 à 05:15, Alyssa Proia <apro...@gmail.com> a écrit :
Has anyone had issues with the GFF pulled from Apollo where sub-feature coordinates extend beyond parent features (e.g., exon extends beyond mRNA), even though the visualization of the features is correct? I have several instances where the sub-feature coordinates are correct, but the feature coordinates are not. Please see attached picture as an example, coordinates are highlighted.Each issue has been with a user-created/edited track. Thanks!
To unsubscribe from this group and stop receiving emails from it, send an email to apollo+un...@lbl.gov.
<Apollo_coordinate_issue.jpg>