I would like to run fastq-dump software (it changes format of DNA sequencing data) and repeat it (when the last process is complete) until all the .sra files in a directory are reformatted to fastq.
I have downloaded a study and the sra files are organize in a series of folders: SRP*\SRS*\SRX*\SRR*\SRA*.sra
I can easily put all the sra files into one folder (if needed) but I can't make fastq-dump do anything more than one-at-time conversion.
For example, currently I am using for the file SRRXXXXX1.sra in the same folder as the fastq-dump app:
fastq-dump --split-files --gzip SRRXXXXX1.sra
I get SRRXXXX1.fastq.gzip but SRRXXXXX2.sra is left alone.
Please help me with batching the conversion!
I wish I could run: fastq-dump --split-files --gzip *.sra
or fastq-dump --split-files --gzip SRP*\SRS*\SRX*\SRR*\SRA*.sra
but it doesn't appear fastq-dump supports *.sra
I am inept at batching files. I just need simple code to run fastq-dump --split-files --gzip SRXXXXX1.sra
and repeat for every single .sra file when the last file is completed (can't do at the same time, it's 200G of data).
This is for windows 7 64 bit.
Edited by Adjuvant, 29 October 2012 - 02:32 PM.