search

oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
330 stars 72 forks source link

Determination of feature type for gff to gtf conversion #304

Closed synanth closed 1 month ago

synanth commented 1 year ago

Hi, I'm exploring this wonderful software as a way to get a comprehensive CHM13 TE annotation file for downstream analysis of RNASeq data. The other bits of software I am using requires gtf, rather than gff, so I am wondering how to determine a reduction mapping between gff's more comprehensive features and gtf's more limited ones. Is it a mechanism of the TE family, or of some other portion of the gff produced by EDTA?

Thank you so much, Synanth

synanth commented 1 year ago

Managed to get it working with AGAT through editing it's associated json files to automatically do the conversion.

oushujun commented 1 year ago

Thanks for opening the issue and providing a solution to the problem!

Best, Shujun

On Wed, Oct 12, 2022 at 10:07 AM Synanth Texocaelum < @.***> wrote:

Closed #304 https://github.com/oushujun/EDTA/issues/304 as completed.

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/304#event-7572269930, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBFDEB6E2ZL2PS7Q7TWC3A33ANCNFSM6AAAAAARBRMNZU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Cjianghao commented 1 month ago

Hi, I'm exploring this wonderful software as a way to get a comprehensive CHM13 TE annotation file for downstream analysis of RNASeq data. The other bits of software I am using requires gtf, rather than gff, so I am wondering how to determine a reduction mapping between gff's more comprehensive features and gtf's more limited ones. Is it a mechanism of the TE family, or of some other portion of the gff produced by EDTA?

Thank you so much, Synanth

Managed to get it working with AGAT through editing it's associated json files to automatically do the conversion. Hi,synanth，I also encountered this problem, how did you ultimately solve it? I haven't solved it yet.

synanth commented 1 month ago

iirc I used AGAT, but I no longer have the script I originally used. It involved changing the mapping parameters in the conversion, but it looks like it may use a yaml format now. Anyways, look into AGAT and see if that works for your use case.