SpatialTE

SpatialTE README

0. DEPENDENCIES

SpatialTE requires the following tools to be installed:

• ST Pipeline v1.7.9 (https://github.com/SpatialTranscriptomicsResearch/st_pipeline)
• Samtools v1.11 (http://www.htslib.org/download/)
• BEDTools v2.29.2 (https://github.com/arq5x/bedtools2/releases)
• R v4 or higher (https://www.r-project.org/)

Also, Python3.8 or higher should be available in your computer.

UPDATE 11/17/2021: For ease of installation of the dependencies, we recommend creating a Conda environment:

conda env create -f SpatialTE.yml 

This will install the appropriate BEDTools, Samtools and R versions. Then, install the ST Pipeline with:

pip install stpipeline==1.7.9

Once downloaded, make sure to grant SpatialTE execution permissions

chmod u+x spatialte_v1.0/*

Afterwards, add the SpatialTE directory to your PATH:

export PATH=$PATH:/path/to/spatialte

1. SETTING UP NECESSARY FILES

If you have not run the ST Pipeline before, you need to generate an index with STAR (version 2.7.6 or higher recommended). For this, I strongly suggest to download the genome FASTA and its corresponding annotation files from UCSC(https://genome.ucsc.edu/).

Additionally, RepeatMasker files (*rm.out) can also be found at the UCSC webpage. A conversion utility between RepeatMasker out file and SpatialTE input TE annotation is also provided. It can be run like this:

convertRMOut_to_SpatialTEinput.sh RepeatMaskerOutfile NameForNewTEFil

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    +

Finally, you need to setup the configuration file (the following sample configuration file is also provided):

#All paths can be absolute or relative
#Path to barcode file 
barcodefile="1000L6_barcodes.txt"

#Path to STAR index with v2.7.6
STARindex="/path/to/mm10_STAR_2.7.6"
#Path to Gene annotation in GTF Format
geneGTFannotation="/path/to/mm10_refGene.gtf"
#Path to TE annotation in BED Format, following the specifications of SpatialTE
TE_bed="mm10_all_from_ucsc.bed"

#Path to Spatial Transcriptomics paired-end FASTQ files
fastq1="spatialtranscriptomics_1.fastq"
fastq2="spatialtranscriptomics__2.fastq"

#Threads to use in STAR and in Samtools
threads=8

#Basename for output directories (no whitespaces)
experimentBasename="experiment_name"

2. RUNNING SPATIALTE

Once everything is set up, you can run the SpatialTE script with the configuration file:

spatialte_v1.0.sh configuration.sh