Dec 19, 2018 · SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data. It comes with Salmon …

In this work, we developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data. We benchmarked our tool against TEtranscripts, a widely used TE …

Dec 11, 2017 · In this work, Baylor College of Medicine researchers have developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data.

#!/usr/bin/env python3 """SalmonTE - Ultra-Fast and Scalable Quantification Pipeline of Transcript Abundances from Next Generation Sequencing Data Usage: SalmonTE.py index [- …

Compared to TEtranscripts, SalmonTE showed a 19x to 27x fold increase in speed. In this analy is, we demonstrate that SalmonTE outperformed TEtranscripts in processing speed. Our …

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data. It comes with Salmon which is a fast …

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances. It is based on snakemake, salmon and R. Note that SalmonTE packages its own …

Furthermore, SalmonTE no longer runs with the older version of snakemake, please update the version of the snakemake package. Regarding #22, mappability for each file is now reported.

Basically, SalmonTE (which was designed to quantify TE expression at the family level) can easily be hijacked to count TE at the locus level instead of the family level. According to the paper, it …

Dec 11, 2017 · SalmonTE – An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data December 11th, 2017