Is there any written script to assemble multiple fastq file from accession id?

Question

[benkhedhermaryem044]

Hi, I am working on 200 set from SRA. I convert SRA files into fastq files

ERR314561_1.fastq ERR314561_3.fastq ERR314575_1.fastq ERR314575_2.fastq .......

and i want to assembled each pair file. So, it would be helpful to have a script to execute this command line of assembly.

a5_pipeline.pl read_1.fastq read_2.fastq mygenome1

Is there any script available?

Answer 1

[benformatics]

I'm confused why you can't just use a basic unix loop for this?

for R1 in *_1.fastq; do echo $R1; R2=${R1//_1.fastq/_2.fastq}; a5_pipeline.pl $R1 $R2 mygenome1; done

I also don't understand why there is a _3.fastq file. Could this be single end file? It is a bit unclear what exactly you are wanting to do here.

[benkhedhermaryem044]

i convert my sra files with fastq-dump , so i have a fastq file with --R1 ---R3 or --R1 --R2... i don have any idea why why there is a R3.fastq file

[Nicolas Rosewick]

barcodes are in R2.fastq ( usually )

[jperezboza]

Are you sure this _2 or _3 are indicative R2? Is it possible you are downloading different files from the same SRA experiment?

[benkhedhermaryem044]

I used SAR toolkit to download SRA file and convert to fastq files.