tecount 0.5.0

Count read alignments on transposable elements subfamilies, families and classes.

TEcount

A package to count reads mapping on transposable elements (TEs) subfamilies, families and classes.

Features

TEcount counts high-throughput sequencing reads aligned on TEs on a reference genome. It reports TE counts by subfamily, family and class on separate outputs. In case of reads aligning on multiple TE loci, it counts only one alignment occurrence for each feature (i.e. subfamily, family or class). It can use single or paired end BAM files, count in strand-specific manner and filter by a minimum read-TE overlap, among other features that can be discovered by running TEcount --help.

Install

TEcount requires python>=3.7, samtools>=1.14 and bedtools>=2.30.0. We strongly recommend installing TEcount, along with its requirements, in a conda environment:

# Create a conda environment with required packages
conda create -n tecount -c conda-forge -c bioconda "python>=3.7" "pip>=21.1" "samtools>=1.14" "bedtools>=2.30.0"

# Clone this repository (and optionally checkout to a specific version)
git clone https://github.com/bodegalab/tecount
cd tecount

# Install the package from the repository using pip from conda environment
conda activate tecount
pip install .

Usage

Requires a BAM file sorted by coordinates and a bed6+3 file with subfamily, family and class in columns 7, 8 and 9.

TEcount -b <sorted_by_coord.bam> -r <rmsk.bed>

Example using test dataset:

TEcount -b ./test/Aligned.sortedByCoord.out.bam  -r ./test/rmsk.GRCm38.chr19.bed.gz

See all available parameters with:

TEcount --help

Acknowledgements

Based on the transposable elements RNA-seq quantification strategy implemented in [1] by Sinha S.

References

1. Marasca, F., Sinha, S., Vadalà, R. et al. LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion. Nat Genet 54, 180–193 (2022). https://doi.org/10.1038/s41588-021-00989-7