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mhammell-laboratory / TEsmall

A pipeline for profiling TE-derived small RNAs
GNU General Public License v3.0
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Incorporation of newer human/mouse genome builds? #4

Closed juanb001 closed 3 years ago

juanb001 commented 4 years ago

Hi,

First off, thanks for providing all the different TE-related tools; they've been really useful!

I was wondering if there were plans to incorporate native support for the latest human/mouse genome builds (hg38/mm10)?

Thanks!

olivertam commented 4 years ago

Hi,

Sorry for the slow response. We're looking into it now.

Thank you for your patience.

juanb001 commented 4 years ago

No worries, thanks for looking into it!

olivertam commented 4 years ago

Hi,

We are hoping to push a few updates on TEsmall code-base as improvements, but if you want to use the software on the newer genome builds, you can download them here. You should be able to download it into the folder with the other genome files. We may set these new genome builds as default when we update the code. Let us know if you have trouble using them.

Thanks.

juanb001 commented 4 years ago

Awesome, thanks for making these builds available. Eager to put this tool to use!

juanb001 commented 4 years ago

Hi again!

I tried running TEsmall by specifying 'hg38' as the genome, but I get a message saying that

tesmall: error: argument -g/--genome: invalid choice: 'hg38' (choose from 'dm3', 'mm9', 'hg19')

Is there a way to specify a custom genome? Or would I need to hack the software and temporarily label my 'hg38' genome as 'hg19'?

olivertam commented 4 years ago

Hi,

Thanks for pointing this out. I just pushed a small update to Github. Would you mind trying it out and letting me know if it fails? We will probably do a more thorough fix in the an upcoming release.

Thanks.

juanb001 commented 4 years ago

I believe it works, thanks!