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)
- Pandas v1.5.0 or higher (https://pandas.pydata.org/)
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,
hg38for human, andmm10for 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 +
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)