QC of fastq files from SRA

Question

[pisiposo84]

I would like to compare my data with the recently published RNAseq of the NCI60 cell line panel SRA

I have used the SRA toolkit to download the SRA files and convert them to fastq, now I will have to submit these fastq files to my analysis pipeline. For the data I have acquired in-house, the fastq files were pre-processed with TrimGalore for adapter trimming. Is it 'safe' to do the TrimGalore pre-processing also on the SRA/fastq files? On the NCBI website, it is not mentioned whether or not the data were already subjected to any QC. Any suggestions?

Answer 1

[jared.andrews07]

Is it safe? Yes. Is it necessary? Run them through FastQC to see if they've been trimmed or have adapters detected.