RNA-SEQ

Question

[ali]

Hi everyone, I am having issues with my RNA-seq data. Specifically, I have data for a single sample that includes two different SRA numbers. Although my data is paired-end, I am uncertain whether each SRR number corresponds to the forward or reverse reads, or if they represent technical replicates. Could someone provide clarification on this matter? SRR10239199 and SRR10239200 for GSM4110156!

Answer 1

[Trivas]

Those are replicates, and if you download the SRR files, you should automatically get R1 and R2 for each SRR.

[ali]

so if I just consider one of the SRR and use fastq-dump --splite -files , its okay ???

[GenoMax]

If you are trying to re-create an analysis and if it used both SRA# then you will need to get both. If you are simply learning/testing then one of SRR may be enough.

[Trivas]

You should be able to do fasterq-dump <SRR number> -O output_folder

[ali]

thanks for your helping