SRA runs: How should I know which run is control and which one is treatment?
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16 months ago
ziziqolo ▴ 10

Hello Biostars, I wnat to prefetch this ERP113326 runs from SRA. But I don't know which run is control, which one is treatment. Whould you please help me to figure out which one is control? Which one is treatment? Many thanks for your answers.

RNA-Seq • 362 views
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16 months ago
kuntalasb ▴ 10

You can just check the library name there. Each SRR/ERR will have a library name, you can identify control/treated samples from there.

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Dear kuntalasb, Thank you for your answer. But would you please explain a bit more? I got confused. I mean that, there are 21 library names for 52 runs. Which one could be control/treat.

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You can go through the description of the bioproject, where generally the treatment type, tissue type etc. are mentioned by the authors/scientists. From the description itself one gets a general idea about the raw SRA data samples. For eg- one would mention the library name for control sample as “untreated_replicate_1” and treated ones as “treated_replicate_2”. Hope this will clear your confusion.

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