Do I need to merge files after downloading them from SRA?

Question

[bioinfo]

Hello,

I am trying to download some files from SRA to perform alignment. One of the samples is https://www.ncbi.nlm.nih.gov/sra?term=SRX3013871 and it consists of two SRR runs. Do I need to merge the files once I have downloaded them?

Thank you

Answer 1

[Istvan Albert]

It all depends on what you wish to do with the results.

The run appears to be the same sample sequenced on the same day probably within the same run.

Normally you would merge the reads.

[bioinfo]

Thank you. I am planning to run FASTQC and then kallisto for allignment. I was thinking of merging the reads but I wanted to be sure.