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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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using TElocal to quantify locus TE expression #42

Open mechealeth opened 2 months ago

mechealeth commented 2 months ago

Hi , I would like to quantify the TE expression from pacbio iso-seq . I directly using minimap2 bam file to run TElocal using --mode uniq, but the ouput file all zero count. I would like to know it is robust to using the TElocal to quantify locus level TE expression in pacbio data. Ang if there any suggestion about this ?

many thanks mincc

olivertam commented 2 months ago

Hi,

Thank you for your interest in the software. Currently, TElocal is designed for short read data, and has not been tested for long reads. We hope to develop something for long read in the near future.

Thanks.

mechealeth commented 2 months ago

Thanks for quick reply ! thanks a lot