multiple SRA to FASTQ conversion

Hello Everyone,
This is a general discussion :slight_smile:

I am currently using SRA and the steps are: 1)Downloading .sra file via prefetch 2) .sra to fastq conversion via fastq-dump.
prefetch command can be used for accession list to download all the SRA files in one go but fastq-dump doesn’t work with accession list (atleast not for me) even though the toolkit has option for using accession list:

any suggestion on how to use toolkit to convert multiple SRA to fastq in one go or need to do it via R or Python?

Hi @Shivani2211,

Just a note that I recategorized this as “Other bioinformatic tools”


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