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Adjuvant

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  1. Hi Guys, 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. Thanks!!!
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