Confusion regarding output data of paired end sequencing run

[discoveradnan]

Hello everyone!

At the end of the run, for a paired end sequencing, does illumina provides two fastq files for right and left reads or single fastq file in which paired end reads are incorporated?

[GenoMax]

Two files. Files have (R1/R2) in their names to indicate the first and second read data.

Not to complicate things further but in some cases R1 and R2 files may be split in individual chunks depending on how the processing was done (and will have additional numbers in the file name to indicate that fact).

[Jessica_L]

To complicate the issue a bit more, using MiSeq reporter, you can stitch reads together assuming you have sufficient overlap between R1 and R2. See here and look for the section on stitching reads at the end of page 7.

[discoveradnan]

Thanks guys