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!
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biolab
1 answer
Yes, that will always work OK.
If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
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.
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