SoloTE README

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)

RepeatMasker files (*rm.out) for several genomes, can be found at the UCSC webpage. A conversion utility is conveniently packaged with SoloTE, in order to tranform the RepeatMasker out file to the BED format required by SoloTE. It can be run like this:

convertRMOut_to_SoloTEinput.sh RepeatMaskerOutfile NameForTEfile

where

• RepeatMaskerOutfile: out file obtained from UCSC or with RepeatMasker
• NameForTEfile: Name for the new, properly formatted, TE annotation file in BED format (required for the pipeline)

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 SpatialTE:

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	3000001	3002128	chr1|3000001|3002128|L1_Mus3:L1:LINE|-	12955	-
chr1	3003153	3003994	chr1|3003153|3003994|L1Md_F:L1:LINE|-	1216	-
chr1	3003994	3004054	chr1|3003994|3004054|L1_Mus3:L1:LINE|-	234	-
chr1	3004041	3004206	chr1|3004041|3004206|L1_Rod:L1:LINE|+	3685	+

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)