Given A Fastq File, Is It Possible To Know If It Comes From Paired Or Single End?

Question

[Pablo Marin-Garcia]

Is there a FASTQ read naming convention for naming paired/single end reads? If it is the case, is this a convention or a format definition?

[Pablo Marin-Garcia]

I have just seen another BioStar question that answer these question (although not directly), and talk about the file names and how the data is spread in different files.

Answer 1

[2184687-1231-83-]

It's "/1" and "/2" at the end of the sequence_id for paired-end data or lack thereof for single fragment, and AFAIK it's a convention.

[brentp]

(assuming illumina) and usually _1.txt and _2.txt as the filenames.

[Pablo Marin-Garcia]

The problem is that I was creating the FASTQ from SRF files, so I was not sure how they manage the paired ends or if they follow any convention, so I wanted to know which are the standard conventions first and see if they were following them.

Answer 2

[Rm]

If reads from multiplexing on the highseq; you will see "/1", "/2" and "/3" ; "/2" is used for the barcode: