What do I do with two SRR Runs per Sample

Question

[James]

For the following data: here, it says that for one sample, there are two runs.

• 2 ILLUMINA (Illumina NovaSeq 6000) runs: 48.8M spots, 4.9G bases, 1.4Gb downloads
• Runs: 2 runs, 48.8M spots, 4.9G bases, 1.4Gb
• • SRR19199897
• • SRR19199898

  What should I do with the data in this case? I used fasterq-dump on both thinking that maybe one was the forward and the other was the reverse for paired-end data, but they both return R1 and R2 reads. Should I use both of these in my analysis or only one? Furthermore, they both have a different number of reads when I use fasterq-dump. Thank!

[aimanbarki]

They are technical repeats. You can use both of them as one sample in the analysis.