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:
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)