Demo 10x Visium dataset for STQ
收藏Zenodo2024-02-13 更新2026-05-26 收录
下载链接：
https://zenodo.org/doi/10.5281/zenodo.10654466
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资源简介：
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} <(cat readnames.list | cut -d '@' -f2) > subset_L001_R1_001.fastqseqtk subseq ${fastq2} <(cat readnames.list | cut -d '@' -f2) > 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.
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Zenodo创建时间：
2024-02-13
