The small dataset includes FASTQ files with 13,043,592 reads from 65 Visium spots of sample WM4237_TE_S1_ST. See https://doi.org/10.1101/2023.07.27.550727 for the full datasets details. Below is the code used to subset FASTQ reads to the 65 spots selected in "subset.csv" fastq1="SC2200092_WM4237-1-1337/fastq/SC2200092_GT22-04384_AGTTTCCTGG-CTGTGTGGCA_S2_L001_R1_001.fastq"fastq2="SC2200092_WM4237-1-1337/fastq/SC2200092_GT22-04384_AGTTTCCTGG-CTGTGTGGCA_S2_L001_R2_001.fastq" fgrep -B 1 -f subset.csv ${fastq1} | grep "@" | cut -d' ' -f1 > readnames.list seqtk subseq ${fastq1} subset_L001_R1_001.fastqseqtk subseq ${fastq2} subset_L001_R2_001.fastq gzip -kv subset_L001_R1_001.fastqgzip -kv subset_L001_R2_001.fastq The data includes output of STQ demo run.