[mira_talk] Quality values for Illumina
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 13 Jul 2011 22:33:55 +0100
On Wednesday, July 13, 2011, Arun Rawat <rawat_arun@xxxxxxxxx> wrote:
>
> Hi Bastein,
>
> The new Illumina software outputs the quality value in offset of 33 ASCII as
> against 84 ASCII offset. Do you think it will affect my cleaning quality if I
> give following CL:qc=yes:qcmq=5:qcwl=5 and what might be the solution for
> this?
>
> Thanks,
> A
Hi,
For the record, you have a typo - the old offset was 64.
Note for Illumina 1.8 the new offset is 33 as per the original Sanger
FASTQ standard.
I think it will be fine as MIRA tries to handle Sanfer/Solexa/Illumina
FASTQ automatically, but there is a switch to set this explicitly if I
recall correctly.
Peter
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