Question: How to get fastq files for individual replicates?
0
gravatar for am010
11 weeks ago by
am0100
am0100 wrote:

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.

rna-seq de next-gen • 139 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by am0100

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.

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by Thind70

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.

ADD REPLYlink written 11 weeks ago by am0100
0
gravatar for AfinaM
11 weeks ago by
AfinaM0
AfinaM0 wrote:

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.

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by AfinaM0

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

ADD REPLYlink written 11 weeks ago by am0100

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

ADD REPLYlink written 11 weeks ago by Thind70
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