Hi everybody, I am doing alignment to 36 PE samples using star. to make it little bit easy task I wrote a bash loop to align them all with the same command. here is my loop:
for i in $(ls raw_data); do STAR --genomeDir index.150 \ --readFilesIn raw_data/$i\_1.fq.gz,raw_data/$i\_2.fq.gz \ --runThreadN 20 --outFileNamePrefix aligned/$i. \ --outSAMtype BAM SortedByCoordinate \ --quantMode GeneCounts \ --sjdbGTFfile GRCm38.90.gtf \ --readFilesCommand zcat ; done
but it seems that something wrong as the alignment took overnight and it was not done yet.