STAR align multiple files

STAR align multiple files

1

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


RNA-Seq


ChIP-Seq


alignment


STAR

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