SequencingFormats

We typically provide the following files/formats as part of a typical data package for HiSeq as well as Genome Analyzer Sequencing Data.

FASTQ Files (Quality Score Files)

This file format is used frequently at the Sanger Institute to bundle a sequence and its quality data.

A Illumina FASTQ file normally uses four lines per sequence:

Line 1 - begins with a '@' character and is followed by a sequence identifier Line 2 - the sequence Line 3 - begins with a '+' character and is optionally followed by the same sequence identifier Line 4 - the quality values for each base in the sequence in Line 2

An Example: @WICMT-SOLEXA_0043:7:1:1500:1199#0/1;1 CTCTGCTGTCTCTTGTGTAAGAAGANANNNCNTTCT +WICMT-SOLEXA_0043:7:1:1500:1199#0/1;1 fffffffRcfad[ddffa]faaaaBBBBBBBBBBBB

The sequence identifier in the above example is "WICMT-SOLEXA_0043:7:1:1500:1199#0/1;1". Please note that the last 2 characters i.e. ";1" may only be found in datasets sequenced by us because we do not remove the filtered reads but indicate them with a 1 (not filtered i.e. good) or 0 (filtered i.e. bad). Please refer to the FAQ's for information on filtering criteria and what it means.

WICMT-SOLEXA	Instrument name
0043	A unique random string for the whole run (pretty much meaningless)
7	flowcell lane
1	tile number within the flowcell lane
1500	'x'-coordinate of the cluster within the tile
1199	'y'-coordinate of the cluster within the tile
#0	index number for a multiplexed sample (0 for no indexing)
/1	the member of a pair, /1 or /2 (paired-end or mate-pair reads only)
;1	Read was not filtered This bit of information is typically not present in FASTQ files created by Illumina pipeline