SoloTE

SoloTE README

0. DEPENDENCIES

SoloTE requires the following tools to be installed, and available in your PATH environment variable:

• Samtools v1.16 or higher (http://www.htslib.org/download/)
• BEDTools v2.29.2 or higher (https://github.com/arq5x/bedtools2/releases)
• R v4 or higher (https://www.r-project.org/)

Also, Python3.9.5 or higher should be available in your computer, along with the following modules:

• Pysam (https://pysam.readthedocs.io/en/latest/installation.html)
• Pandas v1.5.0 or higher (https://pandas.pydata.org/)

1. SETTING UP NECESSARY FILES

RepeatMasker files (*rm.out) for several genomes, can be found at the UCSC webpage. The helper utility, SoloTE_RepeatMasker_to_BED.py, is packed with SoloTE, and it streamlines the download of RepeatMasker file from UCSC, and conversion to BED format. It can be run like this:

python SoloTE_RepeatMasker_to_BED.py -g GenomeVersion

where

• GenomeVersion: genome version identifier. For example, hg38 for human, and mm10 for mouse.

Additionally, the utility can be called with the -l option, and it will list identifiers that can be supplied as the -g parameter, of all available genomes at UCSC (first 5 lines shown next):

python SoloTE_RepeatMasker_to_BED.py -l
ailMel1 | Panda [Ailuropoda melanoleuca, Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)]
allMis1 | American alligator [Alligator mississippiensis, Aug. 2012 (allMis0.2/allMis1)]
anoCar1 | Lizard [Anolis carolinensis, Feb. 2007 (Broad/anoCar1)]
anoCar2 | Lizard [Anolis carolinensis, May 2010 (Broad AnoCar2.0/anoCar2)]
anoGam1 | A. gambiae [Anopheles gambiae, Feb. 2003 (IAGEC MOZ2/anoGam1)]

If you have your own RepeatMasker file and/or a file corresponding to Transposable Elements obtained from another tool, make sure to adapt it to the following format for SoloTE:

sequenceName    startPosition   endPosition sequenceName|startPosition|endPosition|TE_Subfamily:TE_Family:TE_Class|strand   score(optional) .

So, column 4, the ID, is a concatenation of the locus of the TE and its identifiers at the Subfamily, Family and Class level. The file should look like this:

chr1    11505   11675   chr1|11505|11675|L1MC5a:L1:LINE|25.1|-  25.1    -
chr1    11678   11780   chr1|11678|11780|MER5B:hAT-Charlie:DNA|29.4|-   29.4    -
chr1    15265   15355   chr1|15265|15355|MIR3:MIR:SINE|23.0|-   23.0    -
chr1    18907   19048   chr1|18907|19048|L2a:L2:LINE|33.8|+ 33.8    +
chr1    19972   20405   chr1|19972|20405|L3:CR1:LINE|31.2|+ 31.2    +

2. RUNNING SOLOTE

Once everything is set up, you can run the SoloTE script:

python SoloTE_pipeline.py --threads NumberOfThreads --bam BAMfile --teannotation BEDfile --outputprefix Prefix --outputdir OutputDirectory

where

--threads: Number of threads to use

--bam: BAM file

--teannotation: TE annotation in BED format

--outputprefix: Output files prefix

--outputdir: Output directory (if it doesn't exist, it will be created)