illumina fastq reads name

[marinc72]

Hi everyone,
Im a French student so apologize in advance if I make some mistakes .
Im doing a internship and I have a problem understanding something:
I have some fastq files from possum mitochondrion ( strand + and -) and before doing the assembly and mapping process I'v done the "set paired reads by name".
My question is, what means the name of my reads (what information it gives me) and how does it helps in the analysis process ?
example of reads name: FCC68RLACXX:5:1101:16202:2243#/2

Thx in advance

[Brian Bushnell]

Mostly the names are irrelevant and you can ignore them, aside from the trailing "/2" which typically indicates this was a paired-end sequencing run, and this is read 2. There should be another read named "FCC68RLACXX:5:1101:16202:2243#/1" which came from the other end of the same molecule. The numbers typically indicate the physical location of the read on the flowcell, but I don't recognize that specific format. This may be important, because if you are telling a mapping program to detect whether reads are paired based on their names, the exact format tends to be important; for example, Illumina tends to use " /1" and " /2", or " 1" and " 2", to differentiate paired reads.

[nucacidhunter]

In addition to Brian’s comments, naming varies based on CASAVA version. In this example name indicates following:
FCC68RLACXX: Flowcell ID or instrument name
5: lane number
1101: Tile number
16202: X coordinate of cluster
2243: Y coordinate of cluster
2: read number (Read2 of pair)

[Brian Bushnell]

Is there a version of Casava that puts a # before the read number? I assumed it was some 3rd-party software replacing whitespace with non-whitespace.

[nucacidhunter]

I have not seen one, but a variation of this has been described under "Illumina Sequence Identifiers" subheading: http://en.wikipedia.org/wiki/FASTQ_format

[marinc72]

OK I got it, thank for the help to all of you