Question: Is it OK to use --split-files option in fastq-dump when processing SE data?
0
gravatar for biolab
18 months ago by
biolab1.0k
biolab1.0k wrote:

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!

fastq-dump • 616 views
ADD COMMENTlink modified 18 months ago by Devon Ryan86k • written 18 months ago by biolab1.0k
3
gravatar for Devon Ryan
18 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

Yes, that will always work OK.

ADD COMMENTlink written 18 months ago by Devon Ryan86k
1

Thanks a lot, Devon Ryan.

ADD REPLYlink written 18 months ago by biolab1.0k

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

ADD REPLYlink written 18 months ago by WouterDeCoster35k

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

ADD REPLYlink written 18 months ago by genomax59k

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

ADD REPLYlink written 18 months ago by biolab1.0k

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.

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax59k

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

ADD REPLYlink written 18 months ago by biolab1.0k
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