This is a test version of Biostars. For the public version, visit https://www.biostars.org.
QC of fastq files from SRA

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?

rna-seq
• 1,600 views • link
updated by jared.andrews07 jared.andrews07 • written by pisiposo84 pisiposo84

1 answer

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

• 0 views • link
written by jared.andrews07 jared.andrews07

Log in to answer this question.

More posts like this