SRA file identifiers for use with sra-toolkit
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20 months ago
ScubaChris ▴ 10

Greetings,

I have been trying to download some Drosophila samples using the sra-toolkit. However, I am confused as to which identifier should be used each time. For example, the SRA for this sample appears to be DRX013093, however the sra toolkit cannot find it. Clicking on the SRA link will take me to the run page, with the identifier DRR014573. This time, the sra toolkit is able to download the file when given this ID.

My question is, why does the sra-toolkit not understand the first identifier, and is there a way to automate the retrieval of the second identifier?

sra-toolkit • 418 views
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Looks like there are 4 samples in this dataset. You can find them at NCBI here. You should probably just use EBI-ENA to get fastq files. Note that this is 454 data so it may be in colorspace.

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Not sure why it didn't work for you.

[user@desktop ~]$prefetch DRX013093 2020-04-04T19:15:33 prefetch.2.9.2: 1) Downloading 'DRX013093'... 2020-04-04T19:15:33 prefetch.2.9.2: Downloading via https... 2020-04-04T19:16:30 prefetch.2.9.2: 1) 'DRX013093' was downloaded successfully [user@desktop ~]$ cd /tmp/
[user@desktop tmp]$cd sra_test/ [user@desktop sra_test]$ ls
files  nannot  refseq  sra  test  wgs
[user@desktop sra_test]$cd sra/ [user@desktop sra]$ ls
DRX013093.sra

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