10x genomicsのデータからカウントデータを作る方法

# Print line number along with contents of barcodes.tsv.gz and genes.tsv.gz

zcat barcodes.tsv.gz | awk -F "\t" 'BEGIN { OFS = "," }; {print NR,$1}' | sort -t, -k 1b,1 > numbered_barcodes.csv

zcat features.tsv.gz | awk -F "\t" 'BEGIN { OFS = "," }; {print NR,$1,$2,$3}' | sort -t, -k 1b,1 > numbered_features.csv

# Skip the header lines and sort matrix.mtx.gz

zcat matrix.mtx.gz | tail -n +4 | awk -F " " 'BEGIN { OFS = "," }; {print $1,$2,$3}' | sort -t, -k 1b,1 > feature_sorted_matrix.csv

zcat matrix.mtx.gz | tail -n +4 | awk -F " " 'BEGIN { OFS = "," }; {print $1,$2,$3}' | sort -t, -k 2b,2 > barcode_sorted_matrix.csv

# Use join to replace line number with barcodes and genes

join -t, -1 1 -2 1 numbered_features.csv feature_sorted_matrix.csv | cut -d, -f 2,3,4,5,6 | sort -t, -k 4b,4 | join -t, -1 1 -2 4 numbered_barcodes.csv - | cut -d, -f 2,3,4,5,6 > final_matrix.csv

# Remove temp files

rm -f barcode_sorted_matrix.csv feature_sorted_matrix.csv numbered_barcodes.csv numbered_features.csv

https://kb.10xgenomics.com/hc/en-us/articles/360023793031-How-can-I-convert-the-feature-barcode-matrix-from-Cell-Ranger-3-x-to-a-CSV-file-?source=search&auth_token=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJhY2NvdW50X2lkIjo2MTg0NTYsInVzZXJfaWQiOjM3MDEzMzA2NDc5MSwidGlja2V0X2lkIjozNzkwMSwiY2hhbm5lbF9pZCI6NjMsInR5cGUiOiJTRUFSQ0giLCJleHAiOjE1NjI5NzcwOTR9.RoDual95Prc9SimOwu7NIiFZoBWw9OKJShszoO6wlLo

#singlecell

#omics

#informatics