Little question about the datasets you used about sars-cov-2 HOT 4 CLOSED

When using fastq-dump you should include the --split-3 option to put unpaired/orphaned reads into a separate file. Without it, you will have unpaired reads spread throughout your FASTQ files.

For example:

fastq-dump --split-files --split-3 SRR11140750

from sars-cov-2.

We have tried the download with fasterq-dump and now the R1 and R2 reads are even!! We still not get the exact number than the one reported by the authors but we can live with that.
But in case someone has this problem, you have to use sratools >= 2.9

Thanks!

from sars-cov-2.

@saramonzon you can also look at our workflows. We have also prepared histories with already downloaded datasets. See here: https://covid19.galaxyproject.org/1-PreProcessing/#alternate-workflow

from sars-cov-2.

Thank you very much! Happy to see that using --split-3 also does the work! We have already analyzed the data and we are exploring it at the moment!
Thanks for the resources!

from sars-cov-2.