[mira_talk] New Solexa seqence identifier format - Paired end reads

  • From: Alexis Blanchet-Cohen <alexis.blanchet-cohen@xxxxxxxxxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Sat, 14 Apr 2012 21:33:58 +0000


The manual gives instructions on how MIRA will treat paired end reads in Solexa 

However, the identifier format has changed.

Old format: @HWUSI-EAS100R:6:73:941:1973#0/1
New format: @EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG

In the old format, the number 1 at the end of the line indicates which member 
of the paired end read this is.
In the new format, the number 1 is the first number after the space (before the 
Y in this example).

Will MIRA understand the new format?
Do I have to convert the new format to the old format for MIRA to distinguish 
the paired end reads?
If so, what is the sed command to do this?

See Wikipedia for full details of new format for identifier in Solexa FASTQ 
The format of the '@' line has changed since Casava 1.8, according to Wikipedia.

Thank you for your help,

Alexis Blanchet-Cohen

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