Question: How to run STAR for multiple fastq files without overwriting?
0
gravatar for gokberk
7 weeks ago by
gokberk20
gokberk20 wrote:

Hi all,

I'm new to RNAseq data analysis and want to generate BAM files from 204 fastq files. So, I wrote a very basic for loop to run the same command for all my fastq files. However, since STAR saves every BAM file with the same name, I'm having an overwriting problem. Here is the code that I run:

for ((i=102; i<=305; i++)); do ./STAR --readFilesIn fastq/E08/SRR2930$i.fastq --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outSAMmultNmax 1 --genomeDir STARindex --twopassMode Basic --runThreadN 12; done

I tried --outFileNamePrefix option as well, but could not solve the issue. I'd be glad if you could help me with this.

Cheers, Gökberk

star • 183 views
ADD COMMENTlink written 7 weeks ago by gokberk20
3
gravatar for Bastien Hervé
7 weeks ago by
Bastien Hervé4.2k
Limoges, CBRS, France
Bastien Hervé4.2k wrote:

but could not solve the issue.

Please, could you argument the above ?

Did you try something like :

--outFileNamePrefix SRR2930_${i}
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Bastien Hervé4.2k

Previously, I tried --outFileNamePrefix $i, but that didn't work for some reason. now I tried --outFileNamePrefix SRR2930$i and it worked fine, thanks a lot!

ADD REPLYlink written 7 weeks ago by gokberk20
2

$i needs to stay connected to the other word for it not to be treated as a different option. You may want to use --outFileNamePrefix SRR2930_${i} so the names are easier to read.

ADD REPLYlink written 7 weeks ago by genomax67k

I always forget the brackets but they are good practises indeed

ADD REPLYlink written 7 weeks ago by Bastien Hervé4.2k
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