Processing and analysis of spatial transcriptomics datasets generated by Array-seq. The Array-seq cature area size, makes it well-suited for multiple replicates, and high throughput experiments. The ArraySeq package is therefore equipt with functionalities for handling:
- Single tissue sections
- Multiples tissue sections
- Serial sections for 3D spatial transcriptomics
- Sections spacing up to 100 µm have been validated.
Please cite: *Insert Citation Here
After generating fastq files, we recommend using STARSolo (>=2.7.8a) for demulteplexing spatial barcodes and counting UMIs. The barcode.txt file can be downloaded from the Insert folder here folder. Other barcode files from custom-made array designs can be used in its place. Below is an example script for MacOS/Linux:
export PATH=<Path to STAR (>=2.7.8a) static build folder>:$PATH
Fastq_1=<Path to Read1.fastq.gz file>
Fastq_2=<Path to Read2.fastq.gz file>
Sample_name=<Your_Sample_Name>
STAR \
--runThreadN 24 \
--genomeDir <Path to Genome Index Folder> \
--soloType CB_UMI_Simple \
--soloCBwhitelist <Path to n12_barcodes.txt> \
--soloCBstart 1 \
--soloCBlen 12 \
--soloUMIstart 29 \
--soloUMIlen 10 \
--soloBarcodeReadLength 0 \
--soloUMIdedup 1MM_CR \
--soloCBmatchWLtype Exact \
--soloFeatures GeneFull \
--outFilterScoreMinOverLread 0 \
--outFilterMatchNminOverLread 0 \
--clip3pAdapterSeq AAAAAAAAAA \
--clip3pAdapterMMp 0.1 \
--readFilesIn $Fastq_2 $Fastq_1 \
--readFilesCommand zcat \
--soloOutFileNames ${Sample_name}_ST/ features.tsv barcodes.tsv matrix.mtx \
--outFileNamePrefix ${Sample_name}_
gzip ${Sample_name}_ST/GeneFull/raw/*
rm ${Sample_name}_Aligned.out.sam