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Convert in fastq format a list of SRA files

Hello everyone

I have different SRR files in SRA format, how can i covert them into fastq format with cmd? Fastq-dump work on a single SRR file, but my aim is convert every SRR from a certain SRP. I'm able to download the entire SRP with related SRR with pysradb.

Any suggest? Thanks

sra fastq rna-seq
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updated by Ram Ram • written by stefaquara • stefaquara

You can use a loop to go through every file you need to convert or use a more advanced application like gnu parallel to do something more elaborate. If you are working on a cluster you can submit multiple parallel jobs with fastq-dump at the same time.

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written by GenoMax GenoMax

1 answer

Use a loop or GNU parallel to run the conversion serially or in parallel on each file, see the last chunk of code in this tutorial for inspiration (remove the part with prefetch from that code chunk): There are also many other threads on exactly this topic, please search around.

Fast download of FASTQ files from the European Nucleotide Archive (ENA)

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written by ATpoint ATpoint

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