Demo 10x Visium dataset for STQ

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 $fastq1<(catreadnames.list|cut-d^{\prime }{@}^{\prime }-f2)>subse{t}_L{001}_R{1}_{0}01.fastqseqtksubseq${fastq2} <(cat readnames.list | cut -d '@' -f2) > subset_L001_R2_001.fastq

gzip -kv subset_L001_R1_001.fastq
gzip -kv subset_L001_R2_001.fastq

The data includes output of STQ demo run.