gravatar for Manoj

3 hours ago by

United States

Hi,
I have a total of 197 PE samples (R1 and R2). I am trying to run STAR aligner with all these files simultaneously. I am trying with the following command. However, it seems something wrong with this script.
any recommendation
thanks much

for i in $(ls raw_data); do echo /DataAnalysis/STAR-2.7.5a/bin/Linux_x86_64/./STAR --genomeDir 
/DataAnalysis/test-star/SAindex 
--readFilesIn raw_data/${i}_R1.fastq,raw_data/${i}_R2.fastq 
--runThreadN 8 --outFileNamePrefix aligned/$i. 
--outSAMtype BAM SortedByCoordinate 
--quantMode GeneCounts; done

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modified 1 hour ago

by

h.mon31k

written
3 hours ago
by

Manoj80



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