How to run STAR for multiple fastq files without overwriting?
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$i.fastq --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outSAMmultNmax 1 --genomeDir STARindex --twopassMode Basic --runThreadN 12; done
I tried --outFileNamePrefix option as well, but could not solve the issue. I'd be glad if you could help me with this.
Cheers, Gökberk
1 answer
but could not solve the issue.
Please, could you argument the above ?
Did you try something like :
--outFileNamePrefix SRR2930_${i}
• 0 views
•
link
written
by
Bastien Hervé
I always forget the brackets but they are good practises indeed
• 0 views
•
link
written
by
Bastien Hervé
Log in to answer this question.
More posts like this
-
unmapped output of the STAR
written by Wakala •
-
STAR for mouse RNA-seq alignment, which parameters should I use besides the basic ones in practice?
written by FantasticAI •
-
Aligning multiple fastq files with genome in one script/one line with STAR
written by j_eag •
-
star --readFilesIn error when using unmapped.out.mate1/2 files
written by kokoko •
-
snakemake errors and threads
written by Assa Yeroslaviz
-
Problem with generating BAM files with STAR
written by gokberk
-
STAR alignment error: quantmod not found
written by prabin.dm
-
STAR alignment error: ERROR in input reads
written by prabin.dm
-
STAR alignment error- Segmentation fault (core dumped)
written by EagleEye
-
STAR aligner fails to produce unmapped file
written by dec986
(Not exactly answer) You can speed up your command. Your command doesn't mention the "--genomeLoad" method. In that case STAR defaults "NoSharedMemory" i.e loading the index and removing each time you run the command. You can take a look at this post STAR genomeLoad issue.