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
