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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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No comments in TE.gtf allowed #36

Closed foriin closed 5 years ago

foriin commented 5 years ago

Hi! It seems like TEtranscripts fails to generate TE index if there are comments in TE.gtf file. Could you please fix that?

olivertam commented 5 years ago

Hi, Would you be able to provide a copy (or a truncated version) of the TE GTF file that you're using? Was this file generated by us, with comments added afterwards, or generated by you (or another user)? Thanks.

olivertam commented 5 years ago

Hi,

I have made a small fix that might be able to address your issue. If you don't mind re-installing TEtoolkit, either by downloading the ZIP (clicking the clone or download button), or cloning the repository (git clone https://github.com/mhammell-laboratory/tetoolkit.git), you might be able to get it working with your commented TE GTF files.

Feel free to let me know if you hit any issues. Thanks.

foriin commented 5 years ago

Hi, Would you be able to provide a copy (or a truncated version) of the TE GTF file that you're using? Was this file generated by us, with comments added afterwards, or generated by you (or another user)? Thanks.

Sorry it took so long. I used a file from your collection and added simple comment starting with a '#' on a first line. Hope it's resolved in your fix :) Thank you

olivertam commented 5 years ago

Resolved by commit 3754ac9871e47b7814325ffc1725dadc4b616c73