STAR-aligner: genome load in a for-loop
0
0
Entering edit mode
7 weeks ago
Palgrave ▴ 50

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 • 117 views
ADD COMMENT

Login before adding your answer.

Traffic: 2448 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6