TElocal and TEcounts 0.0

[ChiaraGTH]

Dear Oliver Tam,

I am trying to use TElocal tool to find to find transposable elements within my sequence alignments. I have run the following command : TElocal --sortByPos --mode uniq -b SEQ40026_sorted.bam --GTF Danio_rerio.GRCz11.109.gtf --TE /TElocal-master/danRer11_rmsk_TE.gtf.locInd I downloaded the .locInd file from here: https://labshare.cshl.edu/shares/mhammelllab/www-data/TElocal/prebuilt_indices/?C=D;O=A Every time I try, "TE counts total 0.0" appears. And the output table of TElocal contains only 0.

Do you know how I can solve this problem?

Thank you so much.

[olivertam]

Hi,

The issue is that the chromosome names are not the same between danRer11 (which is using UCSC nomenclature) and GRCz11 (which is using Ensembl nomenclature).

We will need to build the TElocal index for that genome build, but if you're using TEcount, you can use the TE GTF provided here, which should work with the genome build you're aligning to.

We will update you once the TElocal index is built.

Thanks.

[ChiaraGTH]

Thank you very much, If I use the GTF file you provided, TE count works perfectly.

[olivertam]

The prebuilt TElocal index for GRCz11 is ready, and can be downloaded here

Thanks