Util folder missing (prepare curated library)

[weilu1998]

Hi,

Thanks for developing this pipeline! I am trying to prepare a curated library for EDTA run based on Dfam curated families. However, I am a bit confused about the class/super family naming requirement, "EDTA/util/TE_Sequence_Ontology.txt" in wiki no longer exist. Where can I find the file with EDTA supported class and super family names?

Also I am wondering would you recommend to use Dfam genus specific (non-model organisms) families as curated library for EDTA?

Thanks,
Wei

[oushujun]

Hi Wei, Until has been migrated to bin, sorry for the confusion. You may use the Dfam library as input for EDTA, but they may not be super helpful if the sequences are highly divergent. Shujun

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On Wed, Dec 25, 2024 at 11:38 PM Phragmites ***@***.***> wrote: Hi, Thanks for developing this pipeline! I am trying to prepare a curated library for EDTA run based on Dfam curated families. However, I am a bit confused about the class/super family naming requirement, "EDTA/util/TE_Sequence_Ontology.txt" in wiki no longer exist. Where can I find the file with EDTA supported class and super family names? Also I am wondering would you recommend to use Dfam genus specific (non-model organisms) families as curated library for EDTA? Thanks, Wei — Reply to this email directly, view it on GitHub <#530>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NFZ6ZAW2K3BPQU5TBT2HOB3HAVCNFSM6AAAAABUGVWKSSVHI2DSMVQWIX3LMV43ASLTON2WKOZSG42TSMRWGQZTOOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[weilu1998]

Hi Wei, Until has been migrated to bin, sorry for the confusion. You may use the Dfam library as input for EDTA, but they may not be super helpful if the sequences are highly divergent. Shujun

Thank you Shujun for the quick reply! If I understand the merging rule 80-80-60 correctly, a slightly more divergent Dfam library shouldn't be detrimental, is that correct? The worst case scenario is that many of the provided Dfam curations not being used. In this case, I am working on the repeat annotation of a butterfly, can I use the whole lepidoptera (~600) + drosophila Dfam (~200) curated libraries?

I also have a unrelated question. Can I filter cds region in an ad-hoc way (start EDTA run without providing cds.fa)? I think the gene annotation might be a bit problematic for my species, for example some cds annotations are actually rDNA. Any suggestions on how to look for potentially misidentified cds in the repeat library?

Thanks,
Wei