Question: Is it OK to use --split-files option in fastq-dump when processing SE data?
0
gravatar for biolab
12 months ago by
biolab1000
biolab1000 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 • 442 views
ADD COMMENTlink modified 12 months ago by Devon Ryan80k • written 12 months ago by biolab1000
3
gravatar for Devon Ryan
12 months ago by
Devon Ryan80k
Freiburg, Germany
Devon Ryan80k wrote:

Yes, that will always work OK.

ADD COMMENTlink written 12 months ago by Devon Ryan80k
1

Thanks a lot, Devon Ryan.

ADD REPLYlink written 12 months ago by biolab1000

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 12 months ago by WouterDeCoster29k

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

ADD REPLYlink written 12 months ago by genomax49k

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

ADD REPLYlink written 12 months ago by biolab1000

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 12 months ago • written 12 months ago by genomax49k

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

ADD REPLYlink written 12 months ago by biolab1000
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