STAR aligner multiple fastq files

Question

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/O24/O24_R1.fastq
/plates/plate_1/rawdata/P24/P24_R1.fastq

It’s 384 sample folders A1, A2, B3, F5,,, so on

Answer 1

It seems the sequencing is single-end, and there is only one fastq per sample. If so:

staridx=/path/to/star/genome/index

mkdir /plates/star/
cd /plates/star/

files=$(find /plates/plate_1/rawdata/ -name "*_R1.fastq")

for i in ${files}
do

  sample=$(basename $i "_R1.fastq")

  STAR --genomeDir $staridx --runThreadN 8 --outFileNamePrefix ${sample}. \
    --readFilesIn $i --outSAMtype BAM

done

All fastq files will be mapped individually, and all bam files will be saved to /plates/star/.