Question: Convert Illumina 1.3 To Illumina 1.5
0
gravatar for Giovanni M Dall'Olio
6.1 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

I have some fastq files in the Illumina 1.3 format. What is the best way to convert it to Illumina 1.5?

Quoting wikipedia, the differences between these two versions is that 1.5 doesn't make use of the symbols "@" and "A" for the phred scores, and that the "B" character has a different meaning:

  ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII......................
  .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ......................
  !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
  |                         |    |        |                              |                     |
                           -5....0........9.............................40 
                                 0........9.............................40 

 I - Illumina 1.3+ Phred+64,  raw reads typically (0, 40)
 J - Illumina 1.5+ Phred+64,  raw reads typically (3, 40)
     with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator

(scheme taken from http://en.wikipedia.org/wiki/FASTQ_format )

Is it safe to simply convert all the "@" and "A" characters to "B"? Or maybe I should convert them all to C?

Should I use:

sed '4~4/[A@]/B/'

or:

sed '4~4/[A@B]/C/'

?

Thanks in advance.

illumina fastq format conversion • 2.1k views
ADD COMMENTlink modified 6.1 years ago by Istvan Albert ♦♦ 82k • written 6.1 years ago by Giovanni M Dall'Olio26k

see http://seqanswers.com/forums/showthread.php?t=5210 ?

ADD REPLYlink written 6.1 years ago by Pierre Lindenbaum125k

Thank you Pierre, but that discussion is about converting Illumina 1.5 to Sanger. Maybe I could do a two-steps conversion 1.5>Sanger>1.3, but if it is possible I would prefer to do it with a single sed script.

ADD REPLYlink modified 6.1 years ago • written 6.1 years ago by Giovanni M Dall'Olio26k
1
gravatar for Istvan Albert
6.1 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

The crux of the problem is what to do with a base that has a quality that is not represented in 1.5 -

that is data with the lowest quality (garbage most likely), since it a useless measurement anyway, so just convert it to the lowest value in 1.5 and that's that - it is wrong anyway

ADD COMMENTlink written 6.1 years ago by Istvan Albert ♦♦ 82k
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