Introduction

The processed scRNA data dowloaded from GEO were alwalys like this.

Files of multiple samples were deposited together. But actually what we want is like follows:

Code exmaple

cd data/GSE184362  # Switch to data directory
ls *matrix.mtx.gz | awk '{split($1,a, "_matrix");printf "mkdir "a[1]"; ""mv "a[1]"* ./"a[1]"/\n"}' > script.sh
ls | grep GSM | awk '{printf "mv "$1"/"$1"_barcodes.tsv.gz "$1"/barcodes.tsv.gz; mv "$1"/"$1"_features.tsv.gz "$1"/features.tsv.gz; mv "$1"/"$1"_matrix.mtx.gz "$1"/matrix.mtx.gz\n"}' > script2.sh
bash script.sh
bash script2.sh

References

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Original

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