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?
/plates/plate_1/rawdata/A1/A1_R1.fastq /plates/plate_1/rawdata/B1/B1_R1.fastq ... /plates/plate_1/rawdata/O24/O24_R1.fastq /plates/plate_1/rawdata/P24/P24_R1.fastq
It’s 384 sample folders A1, A2, B3, F5,,, so on