STAR-aligner: genome load in a for-loop
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12 months ago
Palgrave ▴ 100

I am running multiple samples defined in files.txt. How should I load the genome correctly to avoid it being loaded for each iteration in the loop? I tried the following, but the --genomeLoad LoadAndKeep required fastq-files to be loaded, in addition to the genome.

mapfile -s 1 -t files < files.txt
echo "${files[@]}"

STAR --genomeLoad LoadAndKeep --genomeDir /Genome/


for FILE in ${files[@]}; do
STAR --genomeLoad LoadAndKeep   --quantMode GeneCounts ......;
done



STAR --genomeLoad Remove --genomeDir /Genome/
STAR STAR-aligner • 279 views
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