Illumina results received before August 15th, 2011 (GAII and HiSeq 2000)

Illumina results received before August 15th, 2011 (GAII and HiSeq 2000)

Fastq file name and quality format

These files will be named in the following way: s_lane_read_sequence.txt

For example: s_1_2_sequence.txt

  • lane is the lane that the sample was sequenced in. (1).
  • read is only used for paired-end runs and is 1 for first read or 2 for second read (2).

Unfortunately, in the previous version of data processing pipeline, Illumina does not encode the quality values in the standard (Sanger fastq) way. It is VERY IMPORTANT to note this difference as most downstream tools that will take the fastq file as input (such as an alignment program) will expect the file to be encoded as Sanger fastq.

We highly recommend that you read the wikipedia description of the fastq format that explains the difference between the two different encodings and provides links to software that can convert from one format to the other.

Further information can be found in the following paper: Cock et al (2010) The Sanger FASTQ file format for sequences with quality scores and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 38(6):1767-1771

 

Read names in fastq files

When you open one of your fastq files, you will see that each read has a unique (and rather complicated) name. You are unlikely to need to understand this name, but we provide an explanation so that everything in the fastq file is understandable.

An example of a read ID that you will find in the fastq file is:

PCUS-319-EAS487:7:1:11:495#0/1

This consists of the following elements, separated by ":":

  • MachineName - (hopefully) unique identifier of the sequencer (PCUS-319-EAS487)
  • LaneNumber - positive integer, currently 1-8 (7)
  • TileNumber - positive integer (1)
  • X - x coordinate of the spot. Integer which can be negative (11)
  • Y - y coordinate of the spot. Integer which can be negative (495)
  • #Index - positive integer. No indexing should have a value of 1 (#0)
  • /ReadNumber - 1 for single reads; 1 or 2 for paired ends (/1)

 

 

Published May 26, 2010 1:26 PM - Last modified June 20, 2012 11:50 AM