Producing exactly the same results as TEcount

mhammell-laboratory / TElocal

A package for quantifying transposable elements at a locus level for RNAseq datasets.

GNU General Public License v3.0

21 stars 8 forks source link

Producing exactly the same results as TEcount #1

Closed xunchen85 closed 4 years ago

xunchen85 commented 4 years ago

Hi Oliver,

Thanks for developing the tool. I have installed TElocal, although I got exactly the identical output as TEcount. I don't think I can distinguish each TE locus by using current TElocal/TEcount output. Do you know where I can find the hits at each TE locus?

Best, Xun

olivertam commented 4 years ago

Hi, Are you using the same indices from TEtranscripts? You have to use the ones built for TElocal, which are available here. Thanks.

xunchen85 commented 4 years ago

Thanks,

The help page is confused that allow us to input either GTF or the IND file, probably you can improve it.

I will try it, BTW, the gene annotation should not matter, right?

olivertam commented 4 years ago

Hi, The gene quantification for TElocal currently functions similarly to TEtranscripts, and can use the same gene GTFs. Thanks.

xunchen85 commented 4 years ago

Hi,

Thanks for your prompt response. I will let you know if I have further questions.

Best,