How to get fastq files for individual replicates?

Question

[am010]

Hi All,

I have one confusion regarding fastq files. For example, in the following paper (https://doi.org/10.2983/035.038.0316) the authors have mentioned 3 biological replicates were used for RNA-Seq. They analyzed and compared 3 different conditions and consequently submitted the raw sequence reads as 3 accession numbers viz; SRR7777769, SRR7777770, and SRR7777771. Each of these SRR accesion represents a given condition.

If I download each of these SRR fastq files, I am able to download 6 fastq files (two for each condition) using fasterq-dump because these are paired-ends.

Now I am struggling to understand how to get the raw reads for each biological replicate. Any help will be much appreciated. Thanks in advance.

[Thind amarinder]

usually, all the samples submitted within the specified project (three replicates means 6 fastq files (paired-end) ), Here you can find the details of all the files of a project.

[am010]

Hi, Thanks for your reply. Yes, so that means for 3 conditions it should be 18. If each conditions has 3 biological replicates (As per the paper). Right? But when I download each of these SRR files, I get only 6 fastq files. Two fastq for each condition since these are PE.

Answer 1

[AfinaM]

Hi there,

For each sample, you are able to get 6 fastq files right? Which means there are 3 replicates in there with each replicate has 2 fastq files for paired-ends.

Check the naming of each fastq files, you can see it is written as (sample id)-01 -02 and -03 which indicate the replicates.

[am010]

Hi, Thanks for your reply. No, for each condition only two fastq files are downloaded. Paired-ends.

[Thind amarinder]

Better. contact to author and ask for clarification. sometimes researcher make mistakes at the time of submission.