Issue in exact data download from ENA

Question

[AISHA]

Hi all,

I am facing an issue in choosing a correct fastq file from ENA, since there are two entries for same sample accession (ERS1042158). https://www.ebi.ac.uk/ena/data/view/ERS1042158

Experiment Accession is also same but the Run Accession is different. Can anyone please explain why there are two entries for 1 sample and what could be the possible difference in these two files? File size is also little different (87 GB vs 84 GB).

Thanks!

Answer 1

[ATpoint]

There are sequencing (=same DNA pool, different lanes/flow cells) replicates. Download both, merge fastq files, then align. See here. This is normal for WGS especially in the pre-Novaseq era to split one samples over multiple lanes or flow cells as one lane/FC might not provide reads for the intended average coverage.