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mhammell-laboratory / TElocal

A package for quantifying transposable elements at a locus level for RNAseq datasets.
GNU General Public License v3.0
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Treatment v Control #21

Closed keroguynes closed 1 year ago

keroguynes commented 1 year ago

Hi, I've tried to obtain count table for treatment v. control but the output seems to merge the all the counts in a single column without delineating sample type. I was able to obtain this using TEtranscript and was wondering how to get a similar output with TElocal. I would greatly appreciate any input on this. Thanks in advance.

olivertam commented 1 year ago

Hi,

Thank you for your interest in TElocal.

Unlike TEtranscripts, TElocal operates like TEcount (provided with TEtranscripts) and quantifies each library separately. Thus, to generate the combined count table, you will need to run TElocal on each library, and then join the output (xxxx.cntTable) to make a combined count table.

Please let us know if you have further questions.

Thanks

keroguynes commented 1 year ago

Dear Oliver,

Thank you for your quick response. I have generated count tables for each library. Will join the output as per suggestion.

Many thanks again!