Many SRR files for one experiment. What are the steps to be taken before further analysis?

Question

[cl10101]

I have five SRR files for one sample (five runs, Single read - Illumina experiment). What are the steps to be taken before further analysis? I am converting this files to fastq format. Should I merge this five fastq files before mapping to the genome or map them separately. I am new to NGS and don't fully understand what "runs" means. Should I understand them as five independent experiment repeats and analyse separately?

Answer 1

[microfuge]

Hi Most mappers accept multiple fastq files, so no need of merging them as long as read1 and read2 files are properly supplied. It is also best to retain the original header line of the fastq (-F argument to fastq-dump). See here https://edwards.sdsu.edu/research/fastq-dump/ . The header can be important for FastQC and other downstream applications. SRA classifies as Sample (SRS/ERS) -> Experiment (SRX/ERX) ->Data (SRR/ERR). SRR* files are the resulting data files of a particular experiment (SRX) run on a particular sample (SRP). Running same experiment on the same sample multiple times can result in multiple SRR files.