Question: How to split SRA/fastq files
0
gravatar for Shahzad
2.3 years ago by
Shahzad10
Pakistan
Shahzad10 wrote:

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?

rna-seq next-gen fastq • 1.5k views
ADD COMMENTlink modified 12 months ago by Karma200 • written 2.3 years ago by Shahzad10

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.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax57k

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? Thanks

ADD REPLYlink written 2.3 years ago by Shahzad10

Just like genomax already asked you: please add the SRA number so we can have a look.

ADD REPLYlink written 12 months ago by WouterDeCoster32k
1
gravatar for Karma
12 months ago by
Karma200
India
Karma200 wrote:

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
ADD COMMENTlink modified 12 months ago by genomax57k • written 12 months ago by Karma200
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