using TElocal to quantify locus TE expression

[mechealeth]

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]

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]

Thanks for quick reply ! thanks a lot