SRA-Toolkit 2.3.1 fastq-dump multiplefiles at once Windows command line

[deepbiomed]

Hi Guyz,

I am not software professional so bare with me if I am asking some silly questions.

I have downloaded SRP003329 study, which contains 20 sub-directory with .sra files. Now I am able to convert all these files individually into fastq format using fastq-dump command.
.../bin/fastq-dump -A [ ] -O []
but I want to know how I can do the same for all the .sra files in my dir SRP003329 at once. something like find all .sra files in my directory and fastq-dump all at once.

Thanks
Deep

[jimmybee]

Have you tried:

fastq-dump -A SRP* or

fastq-dump -A *.sra ?

[deepbiomed]

did not work

no it did not work,

Let me tell what I write

/bin/fastq-dump -A [file name] [File path] -O [output path]

now that will convert only one .sra file to fastq file but if I want to do the same for all the file in one dir.,how can I do it or what should I write ?

Thanks
Deep

[GenoMax]

Deep: You will need to write a batch file to do this in one go (from title of your post you are doing this on Windows?). You can search the net for windows batch files to understand how.

If you are a biologist and this is a one time need then bite the bullet and do it the brute force way. If you have spare time and like a good challenge then go the batch file route.

[dpryan]

You might try some of the answers from the thread on biostars that you started (n.b., I forgot an asterisk in the initial version of my answer there). In general, you'll have to script something, which is clunky on windows.

[GenoMax]

Following is not exhaustively tested so use at your own risk. Command as written below assumes that you are in the top study directory (SRP003329), where all the sample sub-directories are present.

for /r %a in (*.sra) do [COLOR="Red"]provide_full_path_to\[/COLOR]fastq-dump.exe %a

This should put all converted "*.fastq" files in SRP003329 directory.

[deepbiomed]

I found this the easiest way to do it. Thanks a lot.