TEtranscripts stopped at TE index building step

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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TEtranscripts stopped at TE index building step #71

Closed hugch2020 closed 4 years ago

hugch2020 commented 4 years ago

Hi, I'm using TEtranscripts 2.1.4 to analyzing TE expression in mouse RNAseq data with mm10_rmsk_TEinst.gtf. The analysis process was held at the "Building TE index" step, the task has been running for a whole day with no error reported. Please give me some suggestions. Thank you Gongcheng

olivertam commented 4 years ago

Hi,

Please use the mm10_rmsk_TE.gtf file instead. The one that you have downloaded is for another program (TElocal), and takes a long time to build.

Thanks.

hugch2020 commented 4 years ago

Yes, I misused the wrong gtf, the new gtf works fine. Thanks.