SequencingFormats
We typically provide the following files/formats as part of a typical data package for HiSeq as well as Genome Analyzer Sequencing Data.
Contents
FASTQ Files (Quality Score Files)
This file format is used frequently at the Sanger Institute to bundle a sequence and its quality data. You will find these files in the "QualityScore" folder of the dataset.
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 |
Technical-Analysis Files
This file is a summary of the alignment results. Please refer to the QC section for more information about this file.
You will only receive this file if a genome alignment was requested.
QC_Report Files
This file summarizes the quality scores (overall as well as per cycle), number of reads and how many were filtered, number of sequences with adaptors and at what position/cycle the adaptor starts as well as the base composition for the entire lane on a cycle by cycles bases for the filtered and unfiltered sets.
Please refer to the QC section for details.
Tag Count Files
These files are created only on request. They have 4 columns:
Column 1 - Sequence Column 2 - Number of occurrences of the sequence in column 1 BEFORE filtering Column 3 - Does the sequence have the 3' adaptor [1 = yes, 0 = No] Column 4 - Number of occurrences of the sequence in column 1 AFTER filtering
