I have an annotation file. I would like to remove redundancy, as shown in the example (in the real file, I have a lot of these redundant cases).

I would like to consider only one of the following genes (the longest could be a good choice). In the case below, the 2 genes have several common exons. As you can see here in the picture, there are two identified genes in the same locus (one identified through Augustus, the other one through GeneMark. They have the same start codon, and the same initial codons, but different final codons and stop codons. Hence, I'd like to retain only one of the two genes:

enter image description here

How can I do that? I have already tried with bedtools, agat_sp_keep_longest_isoform.pl but with no result.

Thanks for the support!

  • $\begingroup$ can you show your attempts with those two tools? $\endgroup$ Commented Jul 25, 2022 at 4:13


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