STAR align multiple files
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.
any recommendation
thanks much
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