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mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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Documentation for reformatting TE GTF file #32

Closed AlicePsyche closed 5 years ago

AlicePsyche commented 5 years ago

Hi,

Sorry for the interruption. I just want to know if there is any guideline for reformatting downloaded UCSC TE GTF file? I found the discussion here and here but it seems that they are not the full rules? For example, for the danRer10, there are 3565006 lines in the rmsk.txt table from UCSC but only 2548675 in your provided GTF file. So what should I do if I want to deal with other organism TE GTF file? (I have to use danRer7, the file is here )

Thanks for your help in advance!

Best, Alice

olivertam commented 5 years ago

Hi Alice,

One filter that we do is to remove structural RNA (e.g. rRNA, scRNA, snRNA, srpRNA, tRNA) and simple repeat/low complexity regions (e.g. (TG)n repeats), as we do not consider them as transposable elements. I think that would account for the differences in numbers. A parsed version of the TE GTF for danRer7 is available (using your file as input) here. Let me know if you are still encountering issues with reformatting or with the provided GTF Thanks.

Cheers, Oliver

AlicePsyche commented 5 years ago

Many thanks for the prompt reply and the ready-to-use GTF file! Really helps me a lot.

GlastonburyC commented 4 years ago

Do any of these filtered GTFs for TEs exist? Because all the links fail for me.

olivertam commented 4 years ago

Hi,

Yes, they exist. Unfortunately, our server might be down right now. We'll post here again once they are up.

Thanks.

olivertam commented 4 years ago

Hi,

The server is back up, and the files should now be accessible.

Thanks for letting us know.

shanshan-yin commented 4 years ago

Hey, the files are unaccessible now again..anyone could help? I need annotation for mouse TEs..

olivertam commented 4 years ago

Hi,

We are having some server issue. We are temporarily hosting files on Dropbox at the following link. Please let us know if you are still having issues accessing the files.

Thanks.