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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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The issue of slow running speed of TEtranscripts #163

Closed cyyisbest closed 7 months ago

cyyisbest commented 7 months ago

Thank you very much for developing this software. I encountered the following issue during the process of running. When I was annotating with TEtranscripts, the server was using a single thread, and it took three days to finish running. I want to ask if there are any actions that can speed up this process.

olivertam commented 7 months ago

Hi,

Thank you for your interest in the software.

We would recommend running TEcount (included with TEtranscripts) on each sample for quantification as a means to parallelize the approach. You can then combine all the output count tables into a single combined count table, and then perform differential analysis with DESeq2.

Thanks.

cyyisbest commented 7 months ago

Thank you very much for your response.