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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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Adding additional transposable elements to annotation file #41

Open R-Najjar opened 1 month ago

R-Najjar commented 1 month ago

Hello, I'd like to search for expression of certain transposable elements that are not in the reference. I added their sequences to the reference fasta, and will see what (if any) aligns to them (using bedtools). If I want to quantify them with TElocal, I will need to also add information about them to the annotation locInd file, correct? How would this work?

Thank you

olivertam commented 1 month ago

Hi,

Thank you for your interest in the software. If you really want to use TElocal in this manner, then you would add their annotation to the TE GTF of your genome build as though their reference sequence is another chromosome. For example:

nonRefTEseqID    custom    exon    1    6500    .    +    .     gene_id "nonRefTE"; transcript_id "nonRefTE_copy1"; family_id "nonRefTE_family"; class_id "nonRefTE_class"

You would then need to build the locInd file yourself using TElocal_indexer. Depending on the size of TE GTF, it could take many days.

Please let me know if this did not address your question.

Thanks.

R-Najjar commented 1 month ago

Thank you Oliver. This makes sense to me