Illumina flowcell to fastq

[ocs]

I'm a bit unsure about the process of getting a fastq-file from an Illumina flowcell. Do they obtain a fastq-file per lane, are there multiple files per lane or can a fastq-file contain multiple lanes?

I wasn't able to find any information on that. Maybe I've missed it, if so, I would appreciate just a link to the source.

Thanks in advance,
Oliver

[GenoMax]

If you have one sample per lane (no multiplexing) you will get the following:

One file per sample - For a single end run
Two Files per sample - for a paired-end run (reads from the two ends of each fragment are in separate files).

If you are multiplexing samples (> 1 sample per lane, appropriately "tagged") then you will still get the same number of files per "tagged" sample after de-multiplexing.

A single fastq file can have multiple samples (not lanes) if you are using an "inline" custom barcode tag scheme. You will then be responsible for de-multiplexing the samples.

I'm a bit unsure about the process of getting a fastq-file from an Illumina flowcell. Do they obtain a fastq-file per lane, are there multiple files per lane or can a fastq-file contain multiple lanes?

I wasn't able to find any information on that. Maybe I've missed it, if so, I would appreciate just a link to the source.

Thanks in advance,
Oliver

[C.R.]

Fastq export and demultiplexing is usually performed with the Illumina CASAVA software: http://support.illumina.com/sequenci...re/casava.ilmn.