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SRA to fastq conversion, 2Gb to 11Gb

Just begin to learn, on youtube, they said after fastq-dump, the file become smaller.

But I am undergoing the other way..my SRA file only 2Gb, after fastq-dump, it become 11Gb...

rna-seq chip-seq
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updated by piet piet • written by bxia bxia

SRA is a compressed file format so if your output fastq file became larger that is not unexpected. As long as the format looks fine don't worry about the file size.
As a sanity check you can search with that SRA accession number at ENA to confirm. ENA provides direct links to fastq files (without having to use sratoolkit).

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written by GenoMax GenoMax

1 answer

But I am undergoing the other way..my SRA file only 2Gb, after fastq-dump, it become 11Gb

FASTQ files are pure ASCII and very large. Thus most people use gzip to shrink their size, typically down to about 20 %. You may want to use the option ' --gzip' with fastq-dump in order to generate gzipped FASTQ.

Moreover, you may also use option '-F' with fastq-dump to shrink the size of the description line.

Finally, fastq-dump produces an extraordinarily verbose variant of FASTQ with the description line doubled for each read. You may want to remove the doubled description line by filtering your FASTQ with a tool like seqtk.

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written by piet piet

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