This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Anyone Using Telescope for Transposable Elements Quantification?

I recently struggled installing SQuIRE for mapping and quantifying Transposable Elements at the locus. I found that Telescope is great at doing it too. I installed it from mlbendall’s github repo. Now I have absolutely no idea of using it. I am trying to find some instances where it was used but none found.

Also, I know SQuIRE used STAR for alignment but Telescope does not directly specify. According to this benchmarking paper, the choice of aligner is open to the researcher to choose. I am not sure how to integrate STAR into Telescope if I want to use STAR for my alignment.

https://academic.oup.com/bib/article/23/1/bbab417/6400501[enter link description here]1 enter link description here

quantification transposable-elements telescope
• 509 views • link
updated by Ram Ram • written by Etornam09 • Etornam09

I found that Telescope is great at doing it too. I installed it from mlbendall’s github repo. Now I have absolutely no idea of using it.

The GitHub repo seems to show how to use the tool (https://github.com/mlbendall/telescope?tab=readme-ov-file#usage ) . As you discovered you can probably use any aligner (if STAR was used then perhaps you want to use aligners that are splice aware).

From the link above:

Basic usage requires a file containing read alignments to the genome and an annotation file with the transposable element gene model.

• 0 views • link
written by GenoMax GenoMax

0 answers

No answers yet.

Log in to answer this question.

More posts like this