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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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multiple core #144

Closed songlyzz closed 10 months ago

songlyzz commented 11 months ago

Hello: I used TEtranscripts to identify differentially expressed genes and TEs in large scale samples. And I found one sample costs ~ 2 hours, can the software use multiple cores to accelerate the speeds like other bioinformatic software such as use the command {-p}? Thank you! And it's very kind of you to develop.

olivertam commented 11 months ago

Hi,

Thank you for your interest in the software. We have considered multi-threading/multi-core, but realize that it significantly complicates the code and makes it unwieldy. One approach to "parallelize" the runs is to use TEcount on each of the samples separately, and then combine the count table output and then run differential analysis. You should be able to take one of the previous TEtranscripts R-code and modify it for your combined count table. Please let me know if you have any questions.

Thanks.

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