Question: Given A Fastq File, Is It Possible To Know If It Comes From Paired Or Single End?
1
gravatar for Pablo Marin-Garcia
7.4 years ago by
Spain
Pablo Marin-Garcia1.8k wrote:

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?

fastq next-gen paired sequencing • 2.5k views
ADD COMMENTlink modified 7.4 years ago by Rm7.8k • written 7.4 years ago by Pablo Marin-Garcia1.8k

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.

ADD REPLYlink written 7.4 years ago by Pablo Marin-Garcia1.8k
6
gravatar for 2184687-1231-83-
7.4 years ago by
2184687-1231-83-4.9k wrote:

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.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by 2184687-1231-83-4.9k
3

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

ADD REPLYlink written 7.4 years ago by brentp22k
1

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.

ADD REPLYlink written 7.4 years ago by Pablo Marin-Garcia1.8k
3
gravatar for Rm
7.4 years ago by
Rm7.8k
Danville, PA
Rm7.8k wrote:

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

ADD COMMENTlink written 7.4 years ago by Rm7.8k
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