Single-end or Paired end reads

Question

[sruthi]

Hi, I downloaded FASTQ files from here . Both the files are in the read files tab of the page. I'm confused with the number of files given and unable to say which file belongs to Read 1 & 2. As the library layout is "PAIRED", should I consider File1 as Read 1 and File 2 as Read 2 or should I check the header of each of the FASTQ files? If latter is the case then File1 : @SRR3929874.1 1/1 File2: @SRR3929874.1 1/2

Or is there any other command to check if the FASTQ file is single end or paired end?

Thanks in advance.

Answer 1

[Arup Ghosh]

It's clearly mentioned in the Library layout column that SRR3929874 is a paired-end library also denoted by @SRR3929874.1 1/2.

Read1: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR392/004/SRR3929874/SRR3929874_1.fastq.gz

Read2: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR392/004/SRR3929874/SRR3929874_2.fastq.gz

[sruthi]

Thanks for your reply.

Answer 2

[GenoMax]

As shown on the ENA page you link: [File 1] contains reads from left end of the fragment being sequenced. [File 2] contain R2 - reads from the right end of the fragments.

Illumina sequence identifiers have taken a couple of different forms when noting paired end reads over the years. They are depicted in Wiki article here.

[sruthi]

Thanks for your reply.