<p>It seems the sequencing is single-end, and there is only one fastq per sample. If so:</p>
<pre><code>staridx=/path/to/star/genome/index

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

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

for i in ${files}
do

  sample=<span class="math-container">$(basename $</span>i &quot;_R1.fastq&quot;)

  STAR --genomeDir <span class="math-container">$staridx --runThreadN 8 --outFileNamePrefix $</span>{sample}. \
    --readFilesIn $i --outSAMtype BAM

done
</code></pre>
<p>All fastq files will be mapped individually, and all bam files will be saved to <code>/plates/star/</code>.</p>

CC BY-SA 4.0
2021-12-08T19:44:47.390Z
2021-12-08T19:44:47.390Z
h.mon
<p>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?</p>
<p>Folder structure:</p>
<pre><code>/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
</code></pre>
<p>It’s 384 sample folders A1, A2, B3, F5,,, so on</p>

CC BY-SA 4.0
2021-03-05T07:13:54.170Z
Thanks I added the path structure
mobasher barsi
<phylogenetics><genome><bash><star><loop>
STAR aligner multiple fastq files
# STAR aligner multiple fastq files

(Asked by: username_0 on 2021-03-04)

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

**Tags:** phylogenetics, genome, bash, star, loop
> **Comments:**
> **username_0**: Thanks I added the path structure  

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## 1 answers

### Answer by username_1 on 2021-12-08. Score: 2

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/.


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