Is it OK to use --split-files option in fastq-dump when processing SE data?

Question

[biolab]

Hi, everyone,

I have a list of SRR accessions and need to process them using Fastq-dump. Some of them are SE, and others are PE data. Do you think it OK to use --split-files option in fastq-dump when processing SE data? I want to use one fastq-dump command to process both SE and PE data (my command is: fastq-dump --split-files <accession>). Thank you very much!

Answer 1

[Devon Ryan]

Yes, that will always work OK.

[biolab]

Thanks a lot, Devon Ryan.

[WouterDeCoster]

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[GenoMax]

Off-label usage of SRAtoolkit commands may be dangerous :)

[biolab]

Hi, genomax, could you please tell me the safe usage of fastq-dump? Thank you very much!

[GenoMax]

That was meant to be a partly humorous comment.

That said, if you know a certain dataset is SE then why use --split-files in first place. In general, search via EBI-ENA to see if the dataset you are looking for is available there since you can directly download fastq files, circumventing need for sratoolkit.

[biolab]

OK, genomax, thanks a lot for your explanations. I will try EBI-ENA.