ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.gz X_2.fastq.gz

Question

[Mr Locuace]

Hello, I am downloading some data from this project from ENA:

https://www.ebi.ac.uk/ena/data/search?query=PRJNA494719

There are cases where I do not understand the format. For instance, this is supposed to be a single-end file (it says "SINGLE"): https://www.ebi.ac.uk/ena/data/view/SRX4809217

but has three files instead, namely, SRR7976417.fastq.gz, SRR7976417_1.fastq.gz and SRR7976417_2.fastq.gz

On the other hand, this file: https://www.ebi.ac.uk/ena/data/view/SRX4809200

is shown as paired-end (says "PAIRED") but is a single file.

For most of the other data in this project, SINGLE has a single file and PAIRED has 3 files (I guess read1, read2, orphan read). For instance:

https://www.ebi.ac.uk/ena/data/view/SRX4809208

and

https://www.ebi.ac.uk/ena/data/view/SRX4809204

How to know if the problematic files are really single-end or paired-end?

Thanks very much

Answer 1

[Sean Davis]

If there are three files, they are paired. The metadata from SRA is not uncommonly incorrect.

[Mr Locuace]

Thank you @Sean Davis !. But what about the single file that says "PAIRED"?. How to know if it is actually single-end or a merge between read1 and read2 paired-ends?

[ATpoint]

Check the read names. If it is a merge you should have the same read name twice (probably adjacent to each other), otherwise read names should be unique.

[Mr Locuace]

Thank you very much @ATpoint !