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I’m using STAR to align fastq files from SMART-seq2. I have raw data folder containing sub-folders with samples names the sub-folders each contain fastq file. How can I make a bash command in order for STAR to go in each of sub-folders and make alignment for the fastq file and retrieve the bam files in one folder? Folder structure: /plates/plate_1/rawdata/A1/A1_R1.fastq /plates/plate_1/rawdata/B1/B1_R1.fastq /plates/plate_1/rawdata/C3/C3_R1.fastq It’s 384 sample folders A1, A2, B3, F5,,, so on Thanks,,

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  • $\begingroup$ Thanks I added the path structure $\endgroup$ – mobasher barsi Mar 5 at 7:13

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