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?
I have just seen (another BioStar question)[http://biostar.stackexchange.com/questions/8565/illlumina-paired-end-reads-file-format] that answer these question (although not directly), and talk about the file names and how the data is spread in different files.
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.
(assuming illumina) and usually _1.txt and _2.txt as the filenames.
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.
If reads from multiplexing on the highseq; you will see "/1", "/2" and "/3" ;
"/2" is used for the barcode: