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original format fastq files #895

Closed sherinesaber closed 1 month ago

sherinesaber commented 5 months ago

Hello, is it possible to use fasterq-dump to download original format fastq files?

prefetch and fastq-dump are too slow.

I tried to prefetch SRR21834810 but it did not work at all. I wanted to prefetch the accession first then use fastq-dump for original fasta format.

wraetz commented 5 months ago

Is it possible to use fasterq-dump to download original format fastq files? No! They have been archived after been converted into a SRA-accession. But they might not have been in fastq-format to begin with. We convert all kinds of formats into SRA-accessions.

Regarding SRR210278808: run this command: vdb-dump SRR210278808 -R1 and see for yourself that there is only one biological read in the accession per spot. The other 2 reads are technical reads. If you want 3 files, run this command: fasterq-dump SRR210278808 --split-files --include-technical

wraetz commented 5 months ago

I just checked SRR21834810, it has also only 1 biological read per spot, but 3 technical ones... I you think there is something wrong with this layout, please contact: sra-tools@ncbi.nlm.nih.gov