I have download a data file from SRA database which contains six fastq run files originally. fastq-dump splits its into 2 files with read1 and read2.
How can I generate six original files from one SRA file?
There is a chance that the submitter's submitted the samples concatenated into just two files. In that case the fastq headers may contain the sample names that could be used to split the samples up. What SRA# are you looking at?
You can search ENA with the accession number you have to see if they have more than 2 fastq files available. You can download fastq files directly from ENA.
I have checked ENA database there are only 2 files with names file1 and file2. I was also thinking that the documents are submitted into 2 files. Is there any way I can separate them OR how to process these files if I have to use them as such?
Just like genomax already asked you: please add the SRA number so we can have a look.
There are options in ENA to download both fastq and .sra files. You can download it one by one and perform following command
fastq-dump --split-3 filename.sra